[gmx-users] mailing list migration
Hi, Today we are migrating the mailinglist server to a new machine, so there might be delays in the delivery of messages. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] If your mails are rejected from the list
Hi everyone, Many users ask why their mails are being automatically rejected from posting. Almost always it's due to one of two reasons: * *The messages are too big*. - Messages*larger than 50KB* are *rejected*. Please include large attachments as *links **for download* from an external ftp server, dropbox etc. * * Mails are sent from an address different from the one you have subscribed with.* - It is important that you subscribe with your mail address *exactly as it appears in the headers* of the mails you send, otherwise your posts will be rejected! /E.g. j...@chem.uni.edu mailto:j...@chem.uni.edu is different from j...@uni.edu mailto:j...@uni.edu joe@gmail.com mailto:joe@gmail.com is different from joe...@gmail.com mailto:joe...@gmail.com/ For subscribing, unsubscribing and editing the settings please visit http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-developers Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [gmx-developers] Wednesday, 15 May: upgrading redmine.gromacs.org
Hi, The new server is up and running. Let us know if you see issues. Cheers, Rossen On 5/12/13 8:56 PM, Rossen Apostolov wrote: Dear users and developers, On Wednesday the redmine server will be upgraded and moved to a new VM. Thus expect downtime of 1-2 hours (if it all goes well :-) ). Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Wednesday, 15 May: upgrading redmine.gromacs.org
Dear users and developers, On Wednesday the redmine server will be upgraded and moved to a new VM. Thus expect downtime of 1-2 hours (if it all goes well :-) ). Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] test, please ignore
test *test* /test/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [gmx-developers] Mails rejected with The message's content type was not explicitly allowed
Hi, There was an issue with /multipart/ missing from the allowed mime types. Now HTML mails should be also accepted. Rossen On 7/5/12 3:24 PM, Rossen Apostolov wrote: Dear all, Recently the Gromacs mailing lists have been used for sending spam and viruses, and thus now only plain text messages are accepted. If you have received rejected mails saying The message's content type was not explicitly allowed it means that you have used in your mail special styles or formatting (e.g. bold typeface, colors etc.). Check your email client settings about how to send messages as plain text, e.g. in GMail make sure to click on Compose - Plain Text. Check also whether a formatted signature is added. Attachments are also not allowed but you could include links for downloads. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about the Gromacs website
Hi all, The root partition of the server was full. It should be working fine now. Cheers, Rossen On 7/15/12 8:03 PM, Justin Lemkul wrote: On 7/15/12 1:59 PM, Andrew DeYoung wrote: Hi, I have been not been able to access http://www.gromacs.org/ today. Has anyone else experienced this? I received the following error message on both Google Chrome and Mozilla Firefox: -- Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. If this is a new install, try refreshing - the API is simply taking its time loading up! HTTP Response Status Code: 500 -- The site goes down once in a while. The redmine site has also been down for a few days. There are probably problems with the server(s). I will contact Rossen; I don't know that he typically reads gmx-users. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CECAM ScalaLife Workshop, Oct 03 - Oct 05, 2012
Dear GROMACS Users, GROMACS is one of the applications participating in the ScalaLife EU project (www.scalalife.eu). ScalaLife is organising a CECAM workshop on High Performance Computing in Computational Chemistry and Molecular Biology: Challenges and Solutions provided by ScalaLife project, between October 3 and 5, in CECAM-HQ-EPFL, Lausanne, Switzerland. ScalaLife has invited renowned life scientists from Europe and USA to discuss recent advances in large scale simulations and showcase their latest results. The workshop will also present the newest developments in three life science software packages: GROMACS, DALTON and DISCRETE. The workshop features multiple hands-on sessions, giving the participants the opportunity to practice the modelling capabilities of the three software packages. These sessions will also include user-clinics, a unique opportunity for users to bring in their own problems and discuss the challenges they face in modelling with the developers of these packages. Registration: = Life-scientist and researchers from academia and industry are cordially invited to participate in the workshop. To apply for participation please go to http://www.cecam.org/workshop-6-672.html or send an email to scalal...@pdc.kth.se * The number of participants is limited. There is no attendance fee. * * Deadline for registration is 1st of September * Coffee breaks, lunches and the workshop dinner listed in the program are covered by the workshop. Agenda: === The detailed program can be downloaded at http://www.scalalife.eu/content/cecam. The short version can be found online at http://www.cecam.org/workshop-2-672.html Location: = A map of EPFL: http://www.cecam.org/upload/misc/EPFL-plan-campus-lausanne.jpg. For more information on how to get to CECAM Headquarters: http://www.cecam.org/lausanne2011.html. Information about nearby hotels will be sent with the confirmation email for your registration. More information about the workshop: http://www.cecam.org/workshop-0-672.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] New maintenance release: 4.5.5
Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz. Some notable updates in this release: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending truncating files to 0 bytes when continuation runs stopped before writing new output. * Fixed COM pulling with multiple constraints checking the convergence of one constraint instead of all. * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms. * AmberGS force field is now based on Amber94 instead of Amber96. * Moved hydrogens in Charmm27 protein termini to separate charge groups and added ACE and CT3 residue types. * Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. * Many small updates to the manual pages of programs. Big thanks to all developers and users! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE
Hi, On 9/13/11 4:27 PM, Mark Abraham wrote: On 14/09/2011 12:20 AM, Marcin Zielinski wrote: Ok, Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during the compilation. Firstly, including config.h inside the fortran .F kernel files for power6 is causing problems with their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a modified xlf.cfg config file for XLF (cppoptions = -P, instead of -C) and pass it on with -F option and then add -qarch=pwr6 (all passed manually) for compilation of each power6 kernel .F file. That fixed the problem with the compilation of Power6 kernels part. Is there any more handy way of doing that? I've noticed that upon using Power6, cmake generates Fortran_DEFINES and Fortran_FLAGS inside src/gmxlib/CMakeFiles/gmx.dir/flags.make file. They somehow can not be modified from the command line. Same goes for the preprocessor flags. (-DCMAKE_CPP_FLAGS do not work?). You can also modify flags by editing CMakeCache.txt and rerunning cmake - if you don't pass options it should preserve what's been already found in the cache file. Secondly, now I get something else: Linking C shared library libmd.so xlc: 1501-218 (W) file ../gmxlib/libgmx.so.6 contains an incorrect file suffix ../gmxlib/libgmx.so.6: In function `__bss_start': (*ABS*+0x1025cb00): multiple definition of `_edata' ../gmxlib/libgmx.so.6: In function `__data_start': (.data+0x8): multiple definition of `__dso_handle' /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtbeginS.o:(.data.rel+0x0): first defined here ../gmxlib/libgmx.so.6: In function `_fini': (.opd+0x30): multiple definition of `_fini' /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x18): first defined here ../gmxlib/libgmx.so.6: In function `_init': (.opd+0x18): multiple definition of `_init' /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x0): first defined here ../gmxlib/libgmx.so.6: In function `_end': (*ABS*+0x10268b20): multiple definition of `_end' ../gmxlib/libgmx.so.6: In function `__bss_start': (*ABS*+0x1025cb00): multiple definition of `__bss_start' /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtendS.o:(.dtors+0x0): multiple definition of `__DTOR_END__' ../gmxlib/libgmx.so.6:(.dtors+0x8): first defined here /usr/bin/ld: error in ../gmxlib/libgmx.so.6(.eh_frame); no .eh_frame_hdr table will be created. make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2 Beats me, sorry. me too :( Rossen Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: inquiry
Please send your mails directly to the mailing list gmx-users@gromacs.org (cc:). Rossen Original Message Subject:inquiry Date: Sun, 17 Jul 2011 01:26:18 -0700 From: sara soleimanzadegan sara_soleimanzade...@yahoo.com Reply-To: sara soleimanzadegan sara_soleimanzade...@yahoo.com To: gmx-users-ow...@gromacs.org gmx-users-ow...@gromacs.org Dear Gromacs users, I'm a beginner in Gromacs and I want to work with martini coarse-grained about surfactant. I studied the tutorial of MARTINI website for protein in water and dspc lipid and etc but I'm a little bit confuse about the .gro file for surfactant. May I know how do produce .gro file for CG structure for surfactant (for example sds) and what are its steps? please help me. Regards S. Soleimanzadegan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Register
You can only register from the website: http://lists.gromacs.org/mailman/listinfo/gmx-users Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] in preparation for 4.5.5 and 4.6 releases
Hi, We are preparing for a new maintenance release 4.5.5. It will fix critical open issues with previous releases, so please file your reports in redmine.gromacs.org by the end of June. After the 4.5.5 release, the stable branch will be frozen for bugfixes only, and new functionality will be added to a new release-4-6-patches branch, a fork of release-4-5-patches right after 4.5.5. Currently the plan is to have in 4.6: * faster native GPU implementation supporting most of current Gromacs features * collective I/O * lambda dynamics and other free energy extensions * AdResS (http://www.mpip-mainz.mpg.de/~poma/multiscale/adress.php) * advanced rotational pulling * file history * several new tools * autoconf removed - support for building only with CMake Code from contributors will be considered for inclusion also but it's necessary that * comes with support for the code in future releases, e.g. port it to the completely new C++ structure in the 5.0 release and maintain it after * builds against 4.5.5 * produces scientifically reliable results * works in parallel and doesn't affect the performance * comes with regression test sets for the new features * has the necessary documentation for usage After 4.5.5 bug fixes need to be applied as: * bugs in 4.5.5: o fix in 4.5.5 - fix in 4.6 - fix in master * bugs in the new features introduced in 4.6: o fix in 4.6 - fix in master The plan is to have 4.5.5 around end of July, and 4.6-gamma a month later. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 2.1
You can try also
$ git tag
release-1-6
release-1-6-01
release-2-0
release-2-0-01
release-2-0-02
release-3-0
release-3-1
release-3-1-1
release-3-1-2
release-3-1-3
release-3-1-4
release-3-2
v4.0.7
v4.5
v4.5-beta1
v4.5-beta2
v4.5-beta3
v4.5-beta4
v4.5.1
v4.5.2
v4.5.3
v4.5.4
# git checkout release-2-0-01
On 6/12/11 11:49 AM, Roland Schulz wrote:
Hi,
you can get it from git. git log {file} shows the history and git
show {version}:{file} gives you a specific version.
In this case you can use:
git show 74b20ce9:src/tools/g_order.c
Is that the official 2.1? We should tag it then.
Rossen
Roland
On Sat, Jun 11, 2011 at 10:11 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca wrote:
Dear users:
Does anybody have the source code for gromacs version 2.1? I would
like to check the original source of g_order, but only versions
3.0 and above are available on the gromacs website.
Thank you,
Chris.
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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Why does the -append option exist?
Hi,
On Jun 4, 2011, at 19:11, Dimitar Pachov dpac...@brandeis.edu wrote:
By the way, is this ever reviewed:
Your mail to 'gmx-users' with the subject
Re: [gmx-users] Why does the -append option exist?
Is being held until the list moderator can review it for approval.
This message usually comes when e.g. one sends mails larger than 50K which are
eventually discarded. If you need to send big attachments post a download link
instead.
Cheers,
Rossen
On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 4/06/2011 8:26 AM, Dimitar Pachov wrote
If this is true, then it wants fixing, and fast, and will get it :-) However,
it would be surprising for such a problem to exist and not have been reported
up to now. This feature has been in the code for a year now, and while some
minor issues have been fixed since the 4.5 release, it would surprise me
greatly if your claim was true.
You're saying the equivalent of the steps below can occur:
1. Simulation wanders along normally and writes a checkpoint at step 1003
2. Random crash happens at step 1106
3. An -append restart from the old .tpr and the recent .cpt file will restart
from step 1003
4. Random crash happens at step 1059
5. Now a restart doesn't restart from step 1003, but some other step
and most importantly, the most important piece of data, that being the
trajectory file, could be completely lost! I don't know the code behind the
checkpointing appending, but I can see how easy one can overwrite 100ns
trajectories, for example, and obtain the same trajectories of size
0.
I don't see how easy that is, without a concrete example, where user error is
not possible.
Here is an example:
[dpachov]$ ll -rth run1* \#run1*
-rw-rw-r-- 1 dpachov dpachov 11K May 2 02:59 run1.po.mdp
-rw-rw-r-- 1 dpachov dpachov 4.6K May 2 02:59 run1.grompp.out
-rw-rw-r-- 1 dpachov dpachov 3.5M May 13 19:09 run1.gro
-rw-rw-r-- 1 dpachov dpachov 2.3M May 14 00:40 run1.tpr
-rw-rw-r-- 1 dpachov dpachov 2.3M May 14 00:40 run1-i.tpr
-rw-rw-r-- 1 dpachov dpachov0 May 29 21:53 run1.trr
-rw-rw-r-- 1 dpachov dpachov 1.2M May 31 10:45 run1.cpt
-rw-rw-r-- 1 dpachov dpachov 1.2M May 31 10:45 run1_prev.cpt
-rw-rw-r-- 1 dpachov dpachov0 Jun 3 14:03 run1.xtc
-rw-rw-r-- 1 dpachov dpachov0 Jun 3 14:03 run1.edr
-rw-rw-r-- 1 dpachov dpachov 15M Jun 3 17:03 run1.log
Submitted by:
ii=1
ifmpi=mpirun -np $NSLOTS
if [ ! -f run${ii}-i.tpr ];then
cp run${ii}.tpr run${ii}-i.tpr
tpbconv -s run${ii}-i.tpr -until 20 -o run${ii}.tpr
fi
k=`ls md-${ii}*.out | wc -l`
outfile=md-${ii}-$k.out
if [[ -f run${ii}.cpt ]]; then
$ifmpi `which mdrun` -s run${ii}.tpr -cpi run${ii}.cpt -v -deffnm
run${ii} -npme 0 $outfile 21
fi
=
From the end of run1.log:
=
Started mdrun on node 0 Tue May 31 10:28:52 2011
Step Time Lambda
51879390 103758.780000.0
Energies (kJ/mol)
U-BProper Dih. Improper Dih. CMAP Dih. LJ-14
8.37521e+034.52303e+034.78633e+02 -1.23174e+032.87366e+03
Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
3.02277e+049.48267e+04 -3.88596e+03 -7.43902e+05 -8.36436e+04
PotentialKinetic En. Total EnergyTemperature Pres. DC (bar)
-6.91359e+051.29016e+05 -5.62342e+053.00159e+02 -1.24746e+02
Pressure (bar) Constr. rmsd
-2.43143e+000.0e+00
DD step 51879399 load imb.: force 225.5%
Writing checkpoint, step 51879590 at Tue May 31 10:45:22 2011
---
Restarting from checkpoint, appending to previous log file.
Log file opened on Fri Jun 3 17:03:20 2011
Host: compute-1-13.local pid: 337 nodeid: 0 nnodes: 8
The Gromacs distribution was built Tue Mar 22 09:26:37 EDT 2011 by
dpachov@login-0-0.local (Linux 2.6.18-194.17.1.el5xen x86_64)
:::
:::
:::
Grid: 13 x 15 x 11 cells
Initial temperature: 301.137 K
Started mdrun on node 0 Fri Jun 3 13:58:07 2011
Step Time Lambda
51879590 103759.180000.0
Energies (kJ/mol)
U-BProper Dih. Improper Dih. CMAP Dih. LJ-14
8.47435e+034.61654e+033.99388e+02 -1.16765e+032.93920e+03
Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.99294e+049.42035e+04 -3.87927e+03 -7.43250e+05 -8.35872e+04
PotentialKinetic En. Total EnergyTemperature Pres. DC (bar)
-6.91322e+051.29433e+05 -5.61889e+053.01128e+02 -1.24317e+02
Pressure (bar) Constr. rmsd
-2.18259e+000.0e+00
DD step 51879599 load
Re: [gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM
Hi, Only OpenMM-2.0 (no CMAP) is supported in the gromacs 4.5 releases. There are no plans at the moment to support all new functionality in OpenMM-3.0. Cheers, Rossen On 5/16/11 9:06 AM, Zhi Wang wrote: On 2011-5-14 0:52, zw...@cam.ac.uk wrote: Hello. I am writing to ask if current GROMACS-GPU supports CMAP dihedrals in CHARMM. We are trying to run GROMACS on GPU. It is mentioned on GROMACS website (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu) that CMAP dihedrals in CHARMM are not support. However, we found it is supported in current OpenMM. Is this problem solved in current GROMACS-GPU version? Cheers, Zhi Hello all, I am not sure this is the suitable place for my question. Or should I post it to gmx-developers? Cheers, Zhi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] git server maintenance downtime
Hi, The git server may be temporarily offline today for maintenance. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] git server maintenance finished
Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the DNS to propagate. The old server is still available at git-old.gromacs.org, 130.237.25.210. We'll take it offline after we make sure the new one runs fine. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: git server maintenance finished
The DNS seems to be finished updating now. Let me know if something doesn't work as expected with the new server. Cheers, Rossen On 5/9/11 5:25 PM, Rossen Apostolov wrote: Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the DNS to propagate. The old server is still available at git-old.gromacs.org, 130.237.25.210. We'll take it offline after we make sure the new one runs fine. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Web site issues (Search, Redmine)
Hi Lutz, On 3/31/11 9:06 PM, Lutz Maibaum wrote: I ran into some issues with the Gromacs web site: 1. I tried to register an account on the bug tracker (http://redmine.gromacs.org/account/register). Upon entering my information, I get the odd error message Email notifications is not included in the list. Perhaps this is related to http://www.redmine.org/issues/7138 ? I moved the server a few days ago and haven't done one of the migration steps. Could you check again and let me know (offline is OK) if it doesn't work? 2. Trying to figure out what's going on, I wanted to check the mailing list archive. Searching for redmine on http://www.gromacs.org/Support/Mailing_Lists/Search gives strange results (just a few emails that are listed dozens of times). That's strange indeed, will fix it. I hope this helps to track some of these things down. Thanks a lot for reporting! Cheers, Rossen Best, Lutz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Various web issues
Hi Justin, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: 1. manual.gromacs.org no longer has any useful content. The site comes up with syrah.cbr.su.se and nothing else. Are there changes going on with this site? I moved the manual to the new server and now it's accessible again. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] New version 4.5.4 of the Gromacs manual
Dear all, The updated version 4.5.4 of the Gromacs manual is available at ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf. Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Various web issues
Hi Justin, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: Hi, I posted this a few days ago, but the problem persists - the search feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very tedious. Right, the search returns total crap. I'll look into that. A couple of other things: 1. manual.gromacs.org no longer has any useful content. The site comes up with syrah.cbr.su.se and nothing else. Are there changes going on with this site? We changed the universities and I moved the www.gromacs.org server along with us, but manual.gromacs.org stayed at the old host (syrah). I'll look put a new one. 2. Sorting features of the mailing list search no longer work. Clicking on the title of any column has no effect. Now it does:) Cheers, Rossen -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Various web issues
Hi again, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: I posted this a few days ago, but the problem persists - the search feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very tedious. The search works again. The search index cache was corrupted and rebuilding it fixed the issue. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] New maintenance release: gromacs-4.5.4
Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. Some notable updates in this release: * Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation Big thanks to all developers and users! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] www site is temporarily down
Hi all, There was a power outage which affected the www.gromacs.org server. The system is being fixed at the moment and therefore unreachable. We expect it to be online soon though. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
Hi, I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith I doesn't matter whether the simulation is short or the system small. You can exclude certain interaction types from the FF but then you'll end up with a most likely meaningless model. Rossen Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is able to use the AMBER forcefield, but it is not possible using gromos force-field. When gromos force-field is used, the output is full of NaN Is that the case? mdrun should complain and exit if the FF isn't supported. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites
Hi, On 12/22/10 4:39 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: Dear Roland: I am not sure what my barrier is electronically, only that there is a barrier. The web site has changed since my last attempt to make modifications, but I still can not add to the site as I once could when it was simply a wiki. Currently, I have a tab labeled [MISSING: skin.common.this-page] and if I click on it there is an edit page option but it is commented out, even when I am logged in. Chris: what is your username at www.gromacs.org? I couldn't find you in the registered users. I fixed the [missing...] label, it was due to unsupervised update of the mindtouch base (we're using a custom skin). To edit the wiki, you have to be added as a contributor by Rossen after you've created your account. This process started when the Gromacs site transitioned over. My suggestion for the documentation and the test suite is that these aspects of gromacs become part of the vision in the way that speed is prioritized. A while back, myself and a colleague had a gromacs pull-code extension turned down as a contribution because it would negatively impact the overall performance of gromacs in the general case. After I mulled that decision over for a while, I realized that it was actually a very good and very important decision made by the developers to keep gromacs as fast as possible over the long term even if that meant losing out on some bells and whistles in the short term. So I would suggest that this philosophy might be usefully applied to code development and that modification acceptance would be dependent on the provision of both documentation and a test suite. Not glamorous, I know, but it's my two-cents and it's why I tend to stay more than a year behind the release cycle with my important runs. Having a proper test suite is indeed very important. After moving to C++ with a different code structure it will be easier to have unit testing of functionality. A speed benchmarking suite is mostly ready too. I tend to be the same way. I will usually play with new features, but I haven't done any production runs with any version post-4.0.7 (mostly due to the fact that I prefer continuity). I agree with this assessment. The need for a test suite that actually works has been debated for a long time, usually amounting to incremental progress at best, but it seems that other MD packages provide extensive tests, though Gromacs does not. I know many are willing to help develop it, and I guess we're waiting on a way to effectively communicate, set priorities and to-do lists, and put it all in motion. Is the Redmine infrastructure on the way? Do we have an estimate on when that might be available? I think it would really help. Actually today I set a testbed for Redmine. I could even import a snapshot of bugzilla so we can preserve old information. We'll probably freeze bugzilla in a read-only mode pretty soon and move everything to redmine. Cheers, Rossen -Justin Thanks again, Chris. -- original message -- sorry I didn't pay attention (was in a hurry). I know that you have helped with the documentation and wouldn't have suggested to you to put it on the wiki if I recognized it was you. I thought it was a new user. And I didn't want to criticize but only point out (to the assumed new user) that the wiki can be improved by everyone. Do you have suggestion of how to improve the documentation or the test suite? What is the barrier to the wiki? I have mentioned that before (on the dev-list) but I think a monthly phone conference could help to coordinate those kind of issues. Roland On Mon, Dec 20, 2010 at 10:07 PM, chris.neale at utoronto.ca wrote: I have changed the topic to continue a conversation that started on cmake -- relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; Dear Roland: It is not my intention to be confrontational, your assistance was very useful, I appreciate it very much, and I realize that it's not your job to comment everything (or even answer my questions on this mailing list). Further, I have actually contributed significantly to the gromacs wiki in the past, but it's not a wiki anymore and the barrier to posting is enough that I'm not the only person who has given up on it. Second, I would like to mention that as a user I am extremely hesitant to upgrade my gromacs version due to the lack of commenting and lack of a good test suite. Anybody who used the free energy code with TIP4P in 2008/2009 or used the pull code in the early versions of gromacs 4 will probably agree with me that testing and documentation are at least as important as new code. I'm not asking anybody else to add documentation or test suites. I'm simply pointing out that gromacs is falling behind in these areas and it is not necessarily a good thing. I think that there is a utility in simply noting
Re: [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU
Hi, On 11/24/10 2:59 AM, lin hen wrote: hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' 1 steps, 20.0 ps. Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.2# Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. * NODE (s) Real (s) (%) Time: 90.796 90.796100.0 1:30 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.060 19.034 1.261* gcq#100: Jesus Can't Save You, Though It's Nice to Think He Tried (Black Crowes) The CPU version running results shows as following: ./mdrun Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.3# Average load imbalance: 4.7 % Part of the total run time spent waiting due to load imbalance: 2.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 % Parallel run - timing based on wallclock. * NODE (s) Real (s) (%) Time: 86.176 86.176100.0 1:26 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:741.634 35.849 20.054 1.197* gcq#0: Thanx for Using GROMACS - Have a Nice Day The gpu version looks *slower *than cpu version, does it make sense? Is there anyway I could optimize? In the default build, the CPU version will use all available cores on the machine and it's faster. 2. For the CPU benchmark dhfr-impl-1nm.bench, when I run : ./mdrun Back Off! I just backed up md.log to ./#md.log.9# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) Starting 16 threads --- Program mdrun, VERSION 4.5.2 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanx for Using GROMACS - Have a Nice Day Where could I modify this nodes#? Give the option -nt to mdrun to specify the number of threads you want to launch, e.g. $ mdrun -nt 8 3. for CPU benchmark dhfr-impl-inf.bench I modified cpu-imp-RF-inf.mdp: nsteps 1 grompp -f cpu-imp-RF-inf.mdp -o topol.tpr it will show: NOTE 1 [file cpu-imp-RF-inf.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... NOTE 2 [file topol.top, line 23568]: System has non-zero total charge: -1.10e+01 GB parameter(s) missing or negative for atom type 'H0' --- Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Everybody's Good Enough For Some Change (LIVE) and when I run ./mdrun the steps still -1, infinite time How could I genete the right topol.tpr? Did you search the mailing lists? Copy and paste the error message in http://www.gromacs.org/Support/Mailing_Lists/Search and you will get a top hit http://lists.gromacs.org/pipermail/gmx-users/2010-September/053764.html You are using grompp 4.5.1 and mdrun 4.5.2 !? Remove all gromacs installs that you have, make a clean 4.5.3 install and try again. Rossen Thanks a lot. YY -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem regarding Gromacs - GPU
Hi, The benchmarks are infinite runs (nsteps=-1). Try adding the -maxh option to mdrun to limit the execution time. Rossen On 11/23/10 9:48 AM, kapil mathur wrote: Dear All, I have some queries regarding the benchmarking result of mdrun-gpu : 1. I have run mdrun-gpu with dhfr-impl-1nm.bench on tesla-c1060 , can you provide me the details regarding the execution time it takes as in my case it is running from a very long time (4-5 hours) . 2. Similar things are happening for Gromacs-MPI also. I am running it as follows : GPU: mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no -s topol.tpr (dhfr-impl-1nm.bench) CPU(Cluster): mpirun -np 4 mdrun -s topol.tpr (dhfr-impl-1nm.bench) Thanking you in advance -- Kapil Mathur HPC Solutions Group C-DAC, Pune Phone: +91-20-25704309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] New release: 4.5.2
Dear Gromacs users and developers, A new maintenance release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz. It fixes: * Double precision energy file reading * CHARMM and GB issues * Support for Altivec (PowerPC) with CMake * Running binaries within the CMake build tree is now possible * Various other fixes Thanks again to all! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [gmx-developers] New release: 4.5.3
Ooops! Made a mistake in the subject, it was supposed to be 4.5.3 :) Rossen On 11/9/10 10:39 PM, Rossen Apostolov wrote: Dear Gromacs users and developers, A new maintenance release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz. It fixes: * Double precision energy file reading * CHARMM and GB issues * Support for Altivec (PowerPC) with CMake * Running binaries within the CMake build tree is now possible * Various other fixes Thanks again to all! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gpu
Hi, Did you read this? http://www.gromacs.org/gpu Rossen On 11/7/10 1:23 PM, Erik Wensink wrote: Dear gmx-users, How to invoke the gpu for simulations, e.g. is there (compiler) flag? Cheers, Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2
Hi, On 11/2/10 1:35 PM, Sander Pronk wrote: Hi Michael, I've just committed a fix to the git repository (it's in the release-4-5-patches branch) There were 2 problems - Energy files in double precision couldn't be read in 4.5.2, due to an overly strict error checking issue. - The box matrix wasn't written out correctly (in any 4.5 version). As Berk said, these issues are bad enough for a new version to be released soon. We'll have one next Monday then! Rossen Sander On 2 Nov 2010, at 11:55 , Michael Brunsteiner wrote: Sander pronk wrote: Hi Michael, I've been able to reproduce both problems - I'll fix them shortly. thanks for your swift reply! I assume any fix will be in the Git version only for some time to come, right? cheers, Michael Sander -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] New release: 4.5.2
Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required) * Made pdb2gmx -chainsep option work * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance. * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output. * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops. * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities. * Fixed corrupted energy and checkpoint file output with BAR free energy calculations. * Fixed normalization of g_density using only the last frame. * Fixed several issues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] User training for Gromacs on parallel systems: a survey
Dear all, Gromacs is participating in the ScalaLife (http://scalalife.org/) European project aimed at improving the parallel performance of Life Science applications. An important part of the ScalaLife project is the dissemination of the results and user training. We have prepared a short questionnaire in order to gather enough information about users and their interests for designing efficient training courses. We will highly appreciate if you could give us your input in the anonymous survey at http://www.surveymonkey.com/s/PBJCJBX. Thank you! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
Hi, On 10/6/10 3:48 AM, Igor Leontyev wrote: Szilárd wrote: The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The result is the same for both the distribution 4.5.1 and git from the release-4-5-patches. See the output bellow. = PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64: CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git You have give as an argument to CMake the path the the gromacs/ directory, not the gromacs/src subdirectory! Rossen CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties): set_target_properties called with incorrect number of arguments. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SwissParam
Thanks for contributing! I added a page about it on the Gromacs website: http://www.gromacs.org/Downloads/Related_Software/SwissParam Rossen On 10/7/10 7:13 PM, Michel Cuendet wrote: SwissParam, a web service that provides topologies and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with the CHARMM or GROMACS softwares: http://swissparam.ch/ The server is fully automatic, and the user only needs to provide the organic molecule of interest in the mol2 format. Topology and parameter files are sent back by e-mail, generally within minutes. For GROMACS users, an itp file is generated for the small molecule, which must be included to the protein or DNA topology produced by GROMACS. A tutorial page explains step by step how to set up a protein-ligand system. Force field parameters are derived from the Merck Molecular ForceField (MMFF). Dihedral angle terms are taken as is, while only the harmonic part of the bond, angle and improper terms are retained (the quartic part is discarded). Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM22. The service is intended for fast and easy force field generation. The parameters have been tested in drug design type of calculations, like docking, minimizations, rapid binding energy estimation (LIECE, MMGB/SA), etc... Deeper parameterizations are probably required for applications in which a finer description of the molecule is required, (e.g. normal mode calculations, ...). SwissParam results can then be used as a starting point for such a procedure. Enjoy SwissParam, and please notify us of any question or suggestion for improvement. Try SwissParam now !! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] an example to test mdrun-gpu x mdrun
Hi Alan, On 9/14/10 3:21 PM, Alan wrote: Hi there, I am testing on a MBP 17 SL 10.6.4 64 bits and nvidia GeForce 9600M GT So I got mdrun-gpu compiled and apparently running, but when I try to run 'mdrun' to compare I have a segment fault. Any other comments to the md.mdp and em.mdp are very welcome too. # To test mdrun-gpu cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md-vv nsteps = 1000 dt = 0.002 constraints = all-bonds constraint-algorithm = shake nstcomm = 1 nstcalcenergy= 1 ns_type = grid rlist= 1.3 rcoulomb = 1.3 rvdw = 1.3 vdwtype = cut-off coulombtype = PME PME on the GPUs is not very fast, about 3 times faster than a single core Tcoupl = Andersen Andersen works only on with OpenMM. Gromacs accepts it as an option but the actual algorithm is not implemented for the CPU version yet. nsttcouple = 1 tau_t= 0.1 tc-grps = system ref_t= 300 Pcoupl = mttk Pcoupltype = isotropic nstpcouple = 1 tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step Fetching date from the GPU every 2 steps is way too often. Use a value that you will actually use in production runs. lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF wget -c http://www.pdbe.org/download/1brv; -O 1brv.pdb pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0 genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p Prot.top -norandom grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr mdrun-gpu -v -deffnm md -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes [snip] Reading file md.tpr, VERSION 4.5.1-dev-20100913-9342b (single precision) Loaded with Money Back Off! I just backed up md.trr to ./#md.trr.7# Back Off! I just backed up md.edr to ./#md.edr.7# WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: Non-supported GPU selected (#0, GeForce 9600M GT), forced continuing.Note, that the simulation can be slow or it migth even crash. Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'PROTEIN G in water' 1000 steps, 2.0 ps. step 900, remaining runtime: 4 s Writing final coordinates. step 1000, remaining runtime: 0 s Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. NODE (s) Real (s) (%) Time: 44.556 44.556100.0 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.027 3.882 6.182 But if I try: mdrun -v -deffnm md -nt 1 [snip] starting mdrun 'PROTEIN G in water' 1000 steps, 2.0 ps. [1]75786 segmentation fault mdrun -v -deffnm md -nt 1 It might be due to the Andersen thermostat setting. Note: using -nt 1 because SHAKE is not supported with domain decomposition. If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu, being my gpu ~2 times slower than only one core. Well, I definitely don't intended to use mdrun-gpu but I am surprised that it performed that bad (OK, I am using a low-end GPU, but sander_openmm seems to work fine and very fast on my mbp). Try fetching data less often. Also, currently the GPUs are best used for implicit solvent simulations BTW, in gmx 4.5 manual, there's reference to Andersen thermostat only at section 6.9 GROMACS on GPUs. Is it supposed to be used only with mdrun-gpu? Yes, at the moment. Rossen Any ideas? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Re: [gmx-users] revive gmx-announce
Hi Inon, That's exactly what we talked about today at a developers' meeting. We'll be posting there announcements! Rossen On 2010-09-15 17.08, Inon Sharony wrote: Hi everyone! I saw that the recent proliferation of GROMACS 4.5 had a hiccup involved (hence 4.5.1), but I only caught this a couple of weeks after it happened (Jewish holidays...) I'm wondering if it would be possible to re-activate the gmx-announce mailing list (or better yet -- reform it as an RSS or atom feed) so that the really important announcements that come out only once-in-a-while could be disseminated without the need to get every post from the users' list. Thanks for your time, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] please help, cannot compile gmx 4.5 openmm
Hi Alan, There was a missing dependency for building gmx_gpu_utils, but for some reason compilation didn't break on linux:) This is now fixed in release-4-5-patches. Pay attention though that the prebuilt OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6 Rossen On 9/11/10 12:56 AM, Alan wrote: I am doing, after compiling and installing the normal grmx 4.5: rm -fr CMakeCache.txt make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON .. make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o Scanning dependencies of target gmx_gpu_utils Linking CXX shared library libgmx_gpu_utils.dylib Undefined symbols: _gmx_strncasecmp, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _debug, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_timed_memtest(int, int)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_quick_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _trim, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- -Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] please help, cannot compile gmx 4.5 openmm
Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. If you get an error as: Linking CXX shared library libopenmm_api_wrapper.dylib ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for i386 which is not the architecture being linked (x86_64) Undefined symbols: OpenMM::State::getVelocities() const, referenced from: snip . then you can force compilation for 32bit by: $ export CFLAGS='-arch i386' $ export CXXFLAGS='-arch i386' or recompile the openmm from source. Rossen On 9/13/10 1:01 PM, Rossen Apostolov wrote: Hi Alan, There was a missing dependency for building gmx_gpu_utils, but for some reason compilation didn't break on linux:) This is now fixed in release-4-5-patches. Pay attention though that the prebuilt OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6 Rossen On 9/11/10 12:56 AM, Alan wrote: I am doing, after compiling and installing the normal grmx 4.5: rm -fr CMakeCache.txt make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON .. make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o Scanning dependencies of target gmx_gpu_utils Linking CXX shared library libgmx_gpu_utils.dylib Undefined symbols: _gmx_strncasecmp, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _debug, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_timed_memtest(int, int)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_quick_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _trim, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- -Rossen -- -Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] git gromacs
On 9/7/10 1:19 PM, Alan wrote: I am trying release-4-5-patches and now I can see it's compiling and installing. However, 'make install' puts the bins only in /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links' or similar to have the gmx bins in /usr/local/bin. I am using cmake. CMake doesn't have a 'make links' target yet. Are there a lot of people who actually use it? Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Please test the new Gromacs-4.5!
Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. A very short lived 4.5 (RIP) :) Rossen On 9/2/10 11:23 AM, Christian Mücksch wrote: Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I get a few errors: - -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work. CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack license resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallLicense.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:707 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack readme resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallInfo.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:708 (cpack_check_file_exists) CMakeLists.txt:40 (include) CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message): CPack welcome resource file: /home/c_muecksch/gpu_Install_Linux/gromacs-4.5/admin/InstallWelcome.txt could not be found. Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/CPack.cmake:709 (cpack_check_file_exists) CMakeLists.txt:40 (include) -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Failed -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Failed -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- No external FFT libraries needed for the OpenMM build, using fftpack! -- Threads not compatible with OpenMM build, disabled! CMake Warning at CMakeLists.txt:183 (message): CPU-based acceleration turned off, OpenMM does not support/need any! -- Looking for include files HAVE_STRING_H -- Looking for include files HAVE_STRING_H - found -- Looking for include files HAVE_MATH_H -- Looking for include files HAVE_MATH_H - found -- Looking for include files HAVE_LIMITS_H -- Looking for include files HAVE_LIMITS_H - found -- Looking for include files HAVE_MEMORY_H -- Looking for include files HAVE_MEMORY_H - found -- Looking for include files HAVE_UNISTD_H -- Looking for include files HAVE_UNISTD_H - found -- Looking for include files HAVE_PWD_H -- Looking for include files HAVE_PWD_H - found -- Looking for include files HAVE_STDINT_H -- Looking for include files HAVE_STDINT_H - found -- Looking for include files HAVE_STDLIB_H -- Looking for include files HAVE_STDLIB_H - found -- Looking for include files HAVE_PTHREAD_H -- Looking for include files HAVE_PTHREAD_H - found -- Looking for include files HAVE_DIRENT_H -- Looking for include files HAVE_DIRENT_H - found -- Looking for include files HAVE_INTTYPES_H -- Looking for include files HAVE_INTTYPES_H - found -- Looking for include files HAVE_REGEX_H -- Looking for include files HAVE_REGEX_H - found -- Looking for include files HAVE_SYS_TYPES_H -- Looking for include files HAVE_SYS_TYPES_H - found -- Looking for include files HAVE_SYS_STAT_H -- Looking for include files HAVE_SYS_STAT_H - found -- Looking for include files HAVE_SYS_TIME_H -- Looking for include files HAVE_SYS_TIME_H - found -- Looking for include files HAVE_RPC_RPC_H -- Looking for include files HAVE_RPC_RPC_H - found -- Looking for include files HAVE_RPC_XDR_H -- Looking for include files HAVE_RPC_XDR_H - found -- Looking for include files HAVE_XMMINTRIN_H -- Looking for include files HAVE_XMMINTRIN_H - found -- Looking for include files HAVE_EMMINTRIN_H -- Looking for include files HAVE_EMMINTRIN_H - found -- Looking for include files HAVE_PMMINTRIN_H -- Looking for include files
Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
On 9/2/10 11:46 AM, Carsten Kutzner wrote: On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote: Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. Hi Rossen, in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is doubly listed. Maybe you want to fix that also. It gives a warning only, though. Thanks Carsten! I fixed that. Strangely, I was getting a warning about it. Rossen Carsten A very short lived 4.5 (RIP) :) Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
Hi Florian, What options did you give to cmake? You have to specify the library name in FFTW3_LIBRARIES, not the lib directory. E.g. $ cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIES=/home/dommert/local/fftw3/lib/libfftw3f.so Rossen On 9/2/10 1:21 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 12:37 PM, Rossen Apostolov wrote: Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different platforms with different compilers * use different MPI and math libraries * use exclusively the CMake build system. Autoconf **will be removed** after this release! * try all new features o Amber and Charmm forcefields o simulated nucleic acids o implicit solvent simulations o Velocity-Verlet integrators, MTTK pressure control and Nose-Hoover chains o Free energy calculations and g_bar * errors/inconsistencies/typos in the documentation If you find any kind of reproducible problems, even minor ones, please file a *bugzilla report *! We will clear them out as soon as possible. If there is no report, we'll assume there is no bug :) This test run will be important for distribution package maintainers - let us know if you have issues specific to your systems. And one more thing - there is a deadline :) We'll try to fix all reports that are filed in *the next two weeks* (i.e by *Sept. 15*)! After that priority will be given to development work on major code restructuring towards 5.0. We're awaiting your reports! Hello, when I try to use CMake I get a bunch of warnings when generating the Makefile: WARNING: Target md requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_luck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_protonate requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_x2top requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxcheck requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxdump requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target gmxpreprocess requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target grompp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target mdrun requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target pdb2gmx requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target tpbconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target do_dssp requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target editconf requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target eneconv requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anadock requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_anaeig requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_analyze requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_angle requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping the item. WARNING: Target g_bar requests linking to directory /home/dommert/local/fftw3/lib. Targets may link only to libraries. CMake is dropping
Re: [gmx-users] Please test the new Gromacs-4.5!
Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /Flo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Please test the new Gromacs-4.5!
On 9/2/10 3:21 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 02:56 PM, Rossen Apostolov wrote: Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi, I downloaded the source again from www.gromacs.org, but unfortunately the same error messages occur, while building works fine. Only the share directory is created and then the installation process stops. Sorry, can you try downloading again:) Rossen /Flo Hi Rossen, thanks for this very helpful information. Compilation works fine now. However when I try to install with make install I get following error message: CMake Error at share/cmake_install.cmake:40 (FILE): file INSTALL cannot find /home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template. Call Stack (most recent call first): cmake_install.cmake:37 (INCLUDE) /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkx/pOUACgkQLpNNBb9GiPkzHgCgs72naoKbpzjNBGWYWhAds6F+ ZyAAmgKf8RDQG39PIEoNIBfX+V7Z3ySS =zTj+ -END PGP SIGNATURE- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs-4.5 (final) is out!
It is finally here: *Gromacs-4.5* has been just released ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.tar.gz. All critical issues have been resolved to deliver a stable and powerful package full of many new features http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5. Big thanks to all developers and users who made it happen! Happy simulating !!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with GPU-Version and implicit water models
Hi, On 08/31/2010 12:53 PM, Christian Mücksch wrote: Dear all, I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only Amber-FF are working in the GPU-version. Gromacs-GPU supports only AMBER and CHARMM forcefields. By default, pdb2gmx enables the -cmap option, and cmap dihedrals are not supported. If you want to use CHARMM, then run as: $ pdb2gmx -f protein.pdb -nocmap. (If you use AMBER then -nocmap is not needed of course) OPLS and Gromos use specific combination rules for nonbonded potential parameters and are not supported. When I want to use the GBSA implicit water-model I have to use cut-off for the electrostatic interactions due to this error-message: This was a bug and I fixed it for the final release. Thank you for reporting! Rossen ERROR 1 [file PR.mdp]: With GBSA, coulombtype must be equal to Cut-off Now, my problem is that the GPU-version does not accept cut-off for the electrostatic interactions since only options like Reaction-Field, Ewald, PME and No-cutoff are supported so I get the following error: --- Program mdrun-gpu_beta, VERSION 4.5-beta4 Source code file: ../gromacs-4.5-beta4/src/kernel/openmm_wrapper.cpp, line: 1038 Fatal error: Internal error: you should not see this message, it means that theelectrosatics option check failed. Please report this error! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Will there be an update allowing to use implicit-water with reaction-field on the GPU? Will it be possible to use other ff like OPLSAA on the GPU? Kind regards, Christian Muecksch -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The last beta release: Gromacs-4.5-beta4
The last beta release of Gromacs-4.5-beta4 is available for download. The AMBER FF have been validated and are now production ready; the GPU code had a serious bug fixed, and there is a new tool g_pme_error (it will be incorporated in g_tune_pme soon though). Most of the critical issues since the previous release have been resolved and we expect to have the final 4.5 within a week or so. There will be no more betas! So please try this release and let us know if you find any problems! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
On 8/19/10 8:51 AM, Berk Hess wrote: Hi, Yes, functiontype 1 and 4 are identical, except that the energy gets added to different terms in the log and energy file. In Gromacs 4.0 (and before) to get a dihedral potential consisting of a sum of cosines with different periodes you could do two things: 1) list multiple proper dihedrals (type 1) in the [ dihedrals ] section 2) use RB dihedrals With 4.5 there is the new option 3) list 1 dihedral type 9 in the [ dihedrals ] section and use multiple entries type 9 in the [ dihedraltypes ] section When converted properly, all three will give the same results. The update I added to the manual is only available through git currently, but there's not much more info than mailed here. I've put an updated manual (-4.5-beta2) on the website: http://www.gromacs.org/Documentation/Manual Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs from git source and openmm failed
Hi, Try it again with the latest release-4-5-branch, Erik added a lot of fixes. Rossen On 8/12/10 1:11 PM, Alan wrote: Hi there, I am trying now to compile mdrun-openmm, by doing: cmake -DGMX_OPENMM=ON .. make mdrun -- Threads not compatible with OpenMM build, disabled CMake Warning at CMakeLists.txt:127 (message): The OpenMM build does not support other acceleration modes! -- Using internal FFT library - fftpack -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental, please report issues -- Configuring done -- Generating done -- Build files have been written to: /Users/alan/Programmes/gromacs/build dhcp-128-232-144-215[2416]:~/Programmes/gromacs/build% make mdrun [ 0%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ... And then I got this error: ... [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: In function ‘nb_kernel400nf_x86_64_sse’: /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: (Each undeclared identifier is reported only once /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: for each function it appears in.) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function) make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] Error 1 make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4.5-beta2 forcefield troubles with the GPU version
Hi, I commited a fix and now all AmberFF are supported with the GPU version. The other forcefields are not supported at the moment. Rossen On 8/10/10 12:19 PM, Karel Berka wrote: Hi all, I am trying to get 4.5-beta2 running on graphic card but mdrun-gpu (gcc 4.1.3) is still complaining about something in forcefields OPLS - The combination rules of the used force-field do not match the one supported by OpenMM: sigma_ij = (sigma_i + sigma_j)/2, eps_ij = sqrt(eps_i * eps_j). Switch to a force-field that uses these rules in order to simulate this system using OpenMM. Amber03 - OpenMM does not support (some) of the provided interaction type(s) (Improper Dih.) Gromos96 53a6 - OpenMM does not support (some) of the provided interaction type(s) (G96 bonds) Charmm27 - OpenMM does not support (some) of the provided interaction type(s) (Improper Dih.) is there any force field which can be used? -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz mailto:karel.be...@upol.cz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gromacs from git source and openmm failed
Hi, On 8/12/10 2:43 PM, Alan wrote: Thanks Rossen, Try it again with the latest release-4-5-branch, Erik added a lot of fixes. Indeed, when I did my report *was* with Erik's mods, which I am afraid, was what broke the compilation. I am using 'git log': Author: Rossen Apostolov ros...@cbr.su.se mailto:ros...@cbr.su.se Date: Thu Aug 12 11:20:18 2010 +0200 Fixed a reverted version string in configure.ac http://configure.ac You have compiled the master branch. During the current release stage all development work and fixes first go in the release-4-5-patches branch, as I wrote. Later those fixes will be merged in the master. Since you have already cloned the repository, you should do: $ git checkout -t origin/release-4-5-patches This branch is under heavy development so it may not even compile sometimes. Do regular $ git pull to keep updated. BTW, is there simpler way to say the revision number in git like 'svn info'? If you run $ git log -n 1 commit 617c955b9154e2361b3240ede285f3094e5dc621 Author: Rossen Apostolov ros...@cbr.su.se Date: Thu Aug 12 14:22:45 2010 +0200 OpenMM: added support for AmberFF proper/improper torsion potentials. commit is the identifier that would roughly correspond to a revision in SVN, but the two systems have conceptual differences and the terms are not equivalent. Have a look at some tutorials on the web for a detailed description. Also, mdrun prints out information about the commit it was compiled from: $ mdrun ... :-) mdrun-gpu (-: Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file topol.tpr, VERSION 4.5-beta3-dev-20100812-617c9 (single precision) 617c9 are the first characters of the commit (compare to the git log command above) Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx-developers mailing list search
Hi, I just updated the website and now you can search also the developers mailing list at http://www.gromacs.org/Support/Mailing_Lists/Search_gmx-developers_mailing_list . The quick link on the front page still takes you to the gmx-users list, so after that you have to click again in the menu on the left. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GMXRC missing
Hi, I commited a patch in the latest git. Thanks for reporting, Rossen On 8/10/10 4:13 PM, Ondrej Marsalek wrote: Dear all, I have installed 4.5 beta2 using cmake and it seems that the GMXRC files are missing in the installation. Can anyone confirm this? Best, Ondrej -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New beta release: 4.5-beta3
Hi, I can't compile using CMake - I get undefined references to GSL functions when compiling do_dssp. -lgsl seems to be missing from the linker line. GSL libraries support has been removed from the CMake system, you can use autoconf for now. The GSL and Gromacs licenses are not compatible for binary releases. Another issue is that the CMake build scripts do not seem to honor CFLAGS. The string -fomit-frame-pointer -finline-functions -funroll-all-loops -O3 -DNDEBUG is added to the end of the flags, which causes a problem since the optimization settings are overruled. Sander just commited a patch that will honour the CFLAGS/CXXFLAGS environmental variables, if they are set. However, the CMake system provides a few build types such as Debug and Release, and they come with predefined set of flags which will be appended to your custom settings. In Gromacs the default Release comes with -O3 etc.(what you see above). If you want more control over the flags then you can use: * cmake -i * ccmake * cmake-gui * manually modify CMakeCache.txt (and run $ cmake /path/to/gromacs after without other arguments) Pay attention that variables are called CMAKE_C_FLAGS, CMAKE_C_FLAGS_RELEASE, CMAKE_CXX_FLAGS etc., and those are the ones that you have to modify. I'll extend the section on custom flags on the website. Plus, I think there should be some kind of minimal readme for usage with CMake. Agreed - I asked for that a while ago, and Rossen put some info here http://www.gromacs.org/Developer_Zone/Cmake I added a new INSTALL.cmake file in the source tree, it will be available in the next release. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] broken links
Hi Alan, Those links were pointing to the old wiki. I fixed them and now they refer directly to the original resources. Let us know if the page needs updating. Rossen On 08/11/2010 06:59 PM, Alan wrote: Hi there, I cannot download from http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM any file and link to Gamess-UK seems to be broken as well. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs-4 benchmarking
On 8/10/10 8:40 AM, vivek sharma wrote: Hi There, I want to benchmark the scalability and speed for gromacs-4 on our cluster. I want to know if there is any benchmarking activity already goin on? I have browsed and got benchmarking for gromacs-3 and it seems that gromacs-4 is much more scalable and faster than gromacs-3. Can somebody suggest me with the standard dataset that can be used for benchmarking? thanks, Vivek We have a benchmarking suite under development and we'll post an announcement when it's ready. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon Woodcrest
Hi, This bug is now fixed in git release-4-5-patches (commit 0a31a047f429). Rossen On 8/6/10 11:33 AM, david.groc...@uk.fujitsu.com wrote: Hi, this is the first time I have messaged this group, so please bear with me. I have had little trouble with previous versions (4.0.7 for example), however with this version the pdb2gmx program gives a segmentation fault error if run stand-alone, even with no input. When compiled with debug, idb claims it is a strlen problem in glibc. Running either grompp or mdrun or any other of the executables without any input files merely yields the help screen (as expected). The single precision version works fine with Intel Compiler and MKL ! The double precision version works with GNU compiler and MKL, but I need it to work with Intel When compiling the double precision version 4.0.7, I found that I needed to use the configure option --disable-x86-64-sse For 4.5b2, I have downloaded both the current version from Git (05Aug - 1500 BST), as well as the tar.gz versions and got the same problem. I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux distribution. Here is my configure line ./configure CC=icc CPPFLAGS=-I$MKL_ROOT/include LDFLAGS=-L$MKL_ROOT/lib/ --with-fft=mkl --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double --program-suffix=LD=icc Followed by make -j 4 make install Has anyone else tried this yet ? It seems like a quite trivial bug. Thanks David David Grocutt Environment Health Research Division Fujitsu Laboratories of Europe Phone: +44 (0) 208 606 4533 Fax: +44 (0) 208 606 4539 Email david.groc...@uk.fujitsu.com __ Fujitsu Laboratories of Europe Limited Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE Registered No. 4153469 This e-mail and any attachments are for the sole use of addressee(s) and may contain information which is privileged and confidential. Unauthorised use or copying for disclosure is strictly prohibited. The fact that this e-mail has been scanned by Trendmicro Interscan does not guarantee that it has not been intercepted or amended nor that it is virus-free. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] New beta release: 4.5-beta3
New beta release of gromacs is available for testing: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz. Many bugs have been fixed in this release, mainly double precision support with icc compilers, SSE2. Have a look at the release note on the website for more details. There are still some issues on Windows platofrms that will be resolved before the final release. Please try it out and see if it works as expected! Hopefully there won't be many more betas :)) Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GMXRC missing
Hi Ondrej, I can confirm the problem. We'll fix it for the next release (unfortunately it didn't make it in -beta3). Rossen On 08/10/2010 04:13 PM, Ondrej Marsalek wrote: Dear all, I have installed 4.5 beta2 using cmake and it seems that the GMXRC files are missing in the installation. Can anyone confirm this? Best, Ondrej -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Test
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tests for gmx 4.5
Hi, I'm resending the message below from last week because it didn't make it to the list due to some problem with the server. Rossen - Hi Mark, It will be definitely important to have the regressiontests working properly and extended as the development of Gromacs continues. We discussed that with Berk, and here are some suggestions about the structure of the suite. 1. Make all current tests 3.3.4 compliant. There _is_ actually such a release :) but it hasn't been really announced. I put a link to the tarball on the website, but also if you checkout the releases-3-3-patches branch ,the release is the last commit in that branch: d26be1f4015d974530e8a203e08ade01008e56a8. The bugs that have been fixed since 3.3.3 are now on the website: http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_versions_3.x. Are there other important issues with that code? 2. There is not much point in comparing the tpr's themselves. Not only it becomes problematic with introducing new options etc, but most of all the important point is to make sure that the simulations are reproducible. So instead, check the development binaries (mdrun-dev, grompp-dev etc.) like that: * run mdrun-dev first with the 3.3.4-reference.tpr and compare against 3.3.4-reference.trr/.edr * run grompp-dev to generate a new dev.tpr and * run mdrun-dev with dev.tpr and compare again against 3.3.4-reference.trr/.edr 3. The above will check only features present in 3.3.4 (and before). New .tpr files will be needed for the new features available in later releases. But those will fail to run with older mdrun. But that's OK - if the error is simply reading tpx file (topol.tpr) version 71 with version 40 program, then the test will be skipped and reported as N/A instead of Failed. In that way the suite can be run against any version of mdrun. It might be better to limit the number of steps, lets say 50, but have stricter checking of the error. With longer runs the trajectories will start deviating more anyway. Berk modified yesterday the way gmxcheck compares the virials - now it uses only the diagonal elements of the tensor since the relative tolerance is very different between them and the off-diagonal ones. Also, the .mdp files should be as small as possible. All default values should be stripped to keep the input easy to read. I already did that with all grompp4.mdp files in the complex/ and simple/ tests (and removed the grompp.mdp files), the kernel/* ones are already using very slim inputs. I put the changes in a new branch, origin/temp_mdp, to keep the master clean before we decide what to do. 4. pdb2gmx: There are new FFs in 4.5 that were not present in previous version which should be checked also. Similarly to the mdrun checks, if pdb2gmx returns errors like Library file ffamber99.rtp not found in current dir nor in default directories. (in 4.0) or Could not find force field 'amber98' (in 4.5), then skip the test and mark it as N/A. EncadFF should be removed, and Amber/CHARMM tests added maybe a little later when we're sure the inputs are working fine. Finally, when all the tests pass with 4.5 we can incorporate them within CTest (there is a very basic support at the moment) and we'll have a nice testing system:) Any comments are welcome. Rossen On 8/4/10 6:08 PM, Mark Abraham wrote: I'm glad there's some interest in the test set. I'm happy to update what I did for 4.0.7 for 4.5 also, but there are a number of issues that need attention from someone other than me. I listed those that occurred to me here http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html, linked also from the Test Set page on the website. Among those issues is that we need a single GROMACS version that produces reliable reference data for all cases we wish to test! Various of the 3.3.x series have known issues that make test set maintenance awkward. If I do the necessary updates to release-3-3-patches branch to make a hypothetical GROMACS 3.3.4 that is useful for making test set reference calculations, should we make such a release? Alternatively, we can just announce that the reference data was generated by the 3-3-version with a given git hash and not release. Thoughts? Mark - Original Message - From: Rossen Apostolov rossen.aposto...@cbr.su.se Date: Wednesday, August 4, 2010 17:56 Subject: Re: [gmx-users] tests for gmx 4.5 To: gmx-users@gromacs.org Hi, The tests haven't been ported to 4.5 yet but I hope to fix that before the final release. Rossen On 7/31/10 7:08 PM, Alan wrote: Is there a proper set of tests for gmx 4.5 because neither ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or git clone git://git.gromacs.org/regressiontests.git http://git.gromacs.org/regressiontests.git is working due to the several modifications done in gmx 4.5 including automatic thread for mdrun (I am using a Mac
Re: [gmx-users] tests for gmx 4.5
Hi Mark, It will be definitely important to have the regressiontests working properly and extended as the development of Gromacs continues. We discussed that with Berk, and here are some suggestions about the structure of the suite. 1. Make all current tests 3.3.4 compliant. There _is_ actually such a release :) but it hasn't been really announced. I put a link to the tarball on the website, but also if you checkout the releases-3-3-patches branch ,the release is the last commit in that branch: d26be1f4015d974530e8a203e08ade01008e56a8. The bugs that have been fixed since 3.3.3 are now on the website: http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_versions_3.x. Are there other important issues with that code? 2. There is not much point in comparing the tpr's themselves. Not only it becomes problematic with introducing new options etc, but most of all the important point is to make sure that the simulations are reproducible. So instead, check the development binaries (mdrun-dev, grompp-dev etc.) like that: * run mdrun-dev first with the 3.3.4-reference.tpr and compare against 3.3.4-reference.trr/.edr * run grompp-dev to generate a new dev.tpr and * run mdrun-dev with dev.tpr and compare again against 3.3.4-reference.trr/.edr 3. The above will check only features present in 3.3.4 (and before). New .tpr files will be needed for the new features available in later releases. But those will fail to run with older mdrun. But that's OK - if the error is simply reading tpx file (topol.tpr) version 71 with version 40 program, then the test will be skipped and reported as N/A instead of Failed. In that way the suite can be run against any version of mdrun. It might be better to limit the number of steps, lets say 50, but have stricter checking of the error. With longer runs the trajectories will start deviating more anyway. Berk modified yesterday the way gmxcheck compares the virials - now it uses only the diagonal elements of the tensor since the relative tolerance is very different between them and the off-diagonal ones. Also, the .mdp files should be as small as possible. All default values should be stripped to keep the input easy to read. I already did that with all grompp4.mdp files in the complex/ and simple/ tests (and removed the grompp.mdp files), the kernel/* ones are already using very slim inputs. I put the changes in a new branch, origin/temp_mdp, to keep the master clean before we decide what to do. 4. pdb2gmx: There are new FFs in 4.5 that were not present in previous version which should be checked also. Similarly to the mdrun checks, if pdb2gmx returns errors like Library file ffamber99.rtp not found in current dir nor in default directories. (in 4.0) or Could not find force field 'amber98' (in 4.5), then skip the test and mark it as N/A. EncadFF should be removed, and Amber/CHARMM tests added maybe a little later when we're sure the inputs are working fine. Finally, when all the tests pass with 4.5 we can incorporate them within CTest (there is a very basic support at the moment) and we'll have a nice testing system:) Any comments are welcome. Rossen On 8/4/10 6:08 PM, Mark Abraham wrote: I'm glad there's some interest in the test set. I'm happy to update what I did for 4.0.7 for 4.5 also, but there are a number of issues that need attention from someone other than me. I listed those that occurred to me here http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html, linked also from the Test Set page on the website. Among those issues is that we need a single GROMACS version that produces reliable reference data for all cases we wish to test! Various of the 3.3.x series have known issues that make test set maintenance awkward. If I do the necessary updates to release-3-3-patches branch to make a hypothetical GROMACS 3.3.4 that is useful for making test set reference calculations, should we make such a release? Alternatively, we can just announce that the reference data was generated by the 3-3-version with a given git hash and not release. Thoughts? Mark - Original Message - From: Rossen Apostolov rossen.aposto...@cbr.su.se Date: Wednesday, August 4, 2010 17:56 Subject: Re: [gmx-users] tests for gmx 4.5 To: gmx-users@gromacs.org Hi, The tests haven't been ported to 4.5 yet but I hope to fix that before the final release. Rossen On 7/31/10 7:08 PM, Alan wrote: Is there a proper set of tests for gmx 4.5 because neither ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or git clone git://git.gromacs.org/regressiontests.git http://git.gromacs.org/regressiontests.git is working due to the several modifications done in gmx 4.5 including automatic thread for mdrun (I am using a Mac with dual core) and more warnings. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University
Re: [gmx-users] double precision pdb2gmx - 4.5beta2 - segmentation fault - icc compiler (gcc is fine)
This was already reported, there is a bugzilla filed already and we are looking at fixing it. http://bugzilla.gromacs.org/show_bug.cgi?id=495 Rossen On 8/6/10 2:45 PM, david.groc...@uk.fujitsu.com wrote: Has anyone else tried this ? The single precision version is fine with icc. Thanks David __ Fujitsu Laboratories of Europe Limited Hayes Park Central, Hayes End Road, Hayes, Middlesex, UB4 8FE Registered No. 4153469 This e-mail and any attachments are for the sole use of addressee(s) and may contain information which is privileged and confidential. Unauthorised use or copying for disclosure is strictly prohibited. The fact that this e-mail has been scanned by Trendmicro Interscan does not guarantee that it has not been intercepted or amended nor that it is virus-free. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined
Hi Chris, ## what I did: module purge module load gcc/gcc-4.4.0 module load cmake/2.8.0 #need version =2.6.4 module load cuda/cuda-3.1 mkdir gpuexec export OPENMM_ROOT_DIR=/project/pomes/cneale/GPC/exe/OpenMM2.0-Source/exec/openmm cmake /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/*src* -DGMX_OPENMM=ON Here is the problem - you are passing to CMake the wrong path, it should be just /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/ (rather than ...-beta2/*src*) -DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=$(pwd)/gpuexec -DLIB_INSTALL_DIR=$(pwd)/gpuexec ## output CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18 (CUDA_INCLUDE_DIRECTORIES): Unknown CMake command CUDA_INCLUDE_DIRECTORIES. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx 4.5 configure options confusing
Hi, This was a typo in configure.ac, the second line should say --without-qmmm-orca. Fixed it for the next release. Thanks for reporting. Rossen On 7/31/10 12:11 PM, Alan wrote: For gmx 4.5 beta, I see with ./configure --help: --without-qmmm-mopacUse modified Mopac 7 for QM-MM (see website) --without-qmmm-mopacUse ORCA for QM-MM What that really means? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tests for gmx 4.5
Hi, The tests haven't been ported to 4.5 yet but I hope to fix that before the final release. Rossen On 7/31/10 7:08 PM, Alan wrote: Is there a proper set of tests for gmx 4.5 because neither ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or git clone git://git.gromacs.org/regressiontests.git http://git.gromacs.org/regressiontests.git is working due to the several modifications done in gmx 4.5 including automatic thread for mdrun (I am using a Mac with dual core) and more warnings. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?
Hi Chris, Actually this was a mistake on the website, it must be CMake = 2.6.4, so 2.8.0 is fine. Although the build system requires CUDA 3.1, that doesn't seem to be the problem from your log. Did you get it to work? Rossen On 08/03/2010 01:06 AM, chris.ne...@utoronto.ca wrote: Ah, I see that I need version =2.6.4 This info is on the web, but not in the INSTALL_GPU file... perhaps that file could include all of the information found here: http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/Gromacs_on_GPUs Thanks, Chris. -- original message -- It seems that cmake 2.8.0 is not recent enough? I attempted to compile like this: cd /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2 module purge module load intel module load cuda #cuda 3.0 module load cmake#cmake 2.8.0 export CC=icc export CXX=icpc cmake /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2/src -DGMX_OPENMM=ON -DGMX_THREADS=OFF make mdrun make install-mdrun # Here is the output that I get: -- The C compiler identification is Intel -- The CXX compiler identification is Intel -- Check for working C compiler: /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc -- Check for working C compiler: /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc -- Check for working CXX compiler: /project/scinet/gpc/intel/Compiler/11.1/072/bin/intel64/icpc -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at gmxlib/CMakeLists.txt:110 (install): install TARGETS given no ARCHIVE DESTINATION for static library target gmx. CMake Error at mdlib/CMakeLists.txt:12 (install): install TARGETS given no ARCHIVE DESTINATION for static library target md. CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18 (CUDA_INCLUDE_DIRECTORIES): Unknown CMake command CUDA_INCLUDE_DIRECTORIES. CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 2.8) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run cmake --help-policy CMP. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring incomplete, errors occurred! make: *** No rule to make target `mdrun'. Stop. make: *** No rule to make target `install-mdrun'. Stop. thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] new beta release - gromacs-4.5-beta2
Hi, Several important bugs in the previous beta have been fixed in this new release. Please try it out and let us know if it doesn't work as expected. We plan to have weekly beta releases so that the final stable 4.5 can be rolled out as soon as possible. So, the more bugs are found quickly, the better :) I've put a beta version of the manual (http://www.gromacs.org/Documentation/Manual) also for those who would like to try new features such as implicit solvent. Let us know if you find errors or inconsistencies. Rossen P.S. Again a reminder for developers: bugfixes go in release-4-5-patches, then merge in master if needed (ref. http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS-4.5-beta1 is out!
On 07/31/2010 10:17 PM, ms wrote: As a young GROMACS user, thank you a lot! I just want to ask: On 30/07/10 20:20, Rossen Apostolov wrote: * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. - Is there a 4.5 version of the manual which documents the implicit solvent feature? - It is already tested enough that one can be comfortable (albeit cautious) using it for real work, or does it require a lot of testing, in your opinion? thanks again! m. As far as I know it's production ready code, but still - this is a beta release so I would do some local testing first. I've put an updated version on the website: http://www.gromacs.org/Documentation/Manual Here is the direct link: http://www.gromacs.org/@api/deki/files/101/=manual-4.5-beta1.pdf Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS-4.5-beta1 is out!
After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases called release-4-5-patches. Bugfixes should be applied there **first**, and if needed, merged from that branch into the master after the fix. See http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more information. New features: * 2D decomposition support for PME: improved load balancing with up to 40% overall performance improvement for large systems. * Memory usage is improved for very large systems, allowing simulations of 100 million atoms. * Running on multi-core nodes now automatically uses threads for domain decomposition through the built-in threaded MPI library * GPU computing support * Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default * Full Cmake support. Autoconf/automake will be deprecated after the final 4.5 release! * Full support for 7 AMBER force fields * Support for CHARMM27, including cmap for dihedrals * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. * Support for nucleic acid simulations * Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains * Support for Bennett acceptance ratio (BAR) free energy calculations * Decoupling group setup for free energy * File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD is required) * g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table * Library support for dynamic index groups based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. * g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. * g_membed: a very convenient utility for embedding membrane proteins into equilibrated lipid bilayers Big thanks to all developers, contributors and users! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] potential git server downtime
Hi, Due to construction work in the university building, the source code repository server git.gromacs.org may experience some downtime on Jul 29/30 (Thu/Fri). Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OpenMM
Hi,O On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote: Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the serial code running on CPU is quite different from that of the parallel code running on GPU (.gro files). That is normal. The architectures are different and the algorithms are different so you can't expect numerically identical results. The simulated ensembles should be properly generated though. Looking at the .log file I have also noticed that the energy terms 'Angle', 'Proper Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)', 'Coulomb (SR), 'RF excl', are null for the simulation performed with the parallel code. OpenMM doesn't report individual energy and force terms, only the totals. This is done for efficiency reasons - it saves GPU memory and avoids slow CPU-GPU transfers. Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] On the new web site, how does one make a user contribution?
Hi Бруце, Many users who registered on the old wiki were given a default status of viewers after the transition to the new site. I changed your status and now you should be able to edit pages across the site. Rossen On 03/09/2010 09:15 PM, Bruce D. Ray wrote: I went to the new web site to make a user contribution, and I was not able to find the method to do that. In fact, I even had to create my user ID again that I had on the old web site. With this new web site, how does one go submitting user contributed software? -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with gromacs-openMM
Hi, try to do add the OpenMM library dir to your library path before running make $ export LD_LIBRARY_PATH=/opt/openmm/lib:$LD_LIBRARY_PATH Also, OpenMM support will be officially available in the next Gromacs release (soon). Rossen On 1/27/10 4:28 AM, jorge_quint...@ciencias.uis.edu.co wrote: make[3]: *** No hay ninguna regla para construir el objetivo `/usr/local/openmm/lib/libOpenMM.*', necesario para `grompp'. Alto. make[3]: se sale del directorio `/root/gromacs-4.0.7/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: se sale del directorio `/root/gromacs-4.0.7/src' make[1]: *** [all] Error 2 make[1]: se sale del directorio `/root/gromacs-4.0.7/src' make: *** [all-recursive] Error 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: AW: [gmx-users] Implicit Solvent
Hi Hans, On 01/21/2010 05:54 PM, Hans HEINDL wrote: Hola Deisy, I have used the implicit solvent which is built into mdrun-openmm. It works well: but there are some setbacks: 1. As far as I know it has only been tested with the amber 99 forcefield port for mdrun-openmm. (see http://chemistry.csulb.edu/ffamber/ ) OpenMM will be integrated in the next Gromacs release and implicit solvent simulations will work with any FF supported by Gromacs. and there is no easy way to do a position restraint in mdrun-openmm. I have compared the results of mdrun-openmm using the amber99 ff to a simulation suing sander and the results look well at a first glance Hans -Ursprüngliche Nachricht- *Von:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]*im Auftrag von *deisy yurley rodriguez sarmiento *Gesendet:* Donnerstag, 21. Jänner 2010 17:12 *An:* Gromacs *Betreff:* [gmx-users] Implicit Solvent Hi everyone!!! Can I use implicit solvent in a MD simulations on gromacs? How can I do it? Thanks for your help!!! Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX Tel. 6344000 ext. 2792 Universidad Industrial de Santander -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] searching mailing lists other than gmx-users
Hi, Sure, but the only other list worth searching is the developers list. Rossen Mark Abraham wrote: Hi, As far as I can see, the mailing list search page http://www.gromacs.org/Support/Mailing_Lists/Search only searching gmx-users. While that's a good start, there's often information on the other lists people might wish the option of searching for. Can we have more of a user interface here, please? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Rossen Apostolov Center for Biomembrane Research Department of Biochemistry Biophysics Stockholm University SE-106 91 Stockholm Tel: +46-816-3091 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mailing list search
Update: I set a limit of 500 results from any query. The server shouldn't hang anymore. Rossen Apostolov wrote: Hi, You don't need to register or login if you want to search the mailing list. All searches for words of 3 letters or less, for example pdb, are ignored and you'll get a blank page. There is a problem now with queries that return a lot of hits, for example protein. It does take forever to render the page, and sometimes it times out. I'll look at that and fix it. Rossen seunghwan lee wrote: Hi, I am new to Gromacs and trying to get some info from mailing list. But, mailing list search always returns a blank page or takes forever to finish. It doesn't matter whether I loggin or not. Is there anything that I have to do before using mailing list search? Thanks for your help. Seunghwan Lee ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mailing list search
Hi, I registered yesterday and I am logged in, but perhaps I am not registered as contributor... I added you as a contributor. Thanks for offering to help! New users are only viewers by default to avoid giving instant write permissions to everyone. People who would like to contribute should send me a mail and I'll change their role. There is a note about that in bold on the front page. Rossen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mailing list search
Hi, I made some updates and incorrectly changed the permissions. You should be able to search now even without logging in. Rossen Sun Joo Lee wrote: Hello I have been trying to search the mailing list after I logged in to the new gromacs website. But I do not get any searched results but This page is restricted. comment. Could anyone tell me what the problem might be? Thank you Sunjoo ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Mailing List Search on the new website
Hi Mark and David, I agree with the points you make. The change was rather abrupt but in the long term I believe the dekiwiki will be a much better and useful platform. The dekiwiki has been initially developed on top of mediawiki with the aim to make it more user friendly to modify content, e.g. using a WYSIWYG editor etc. It has very powerful scripting capabilities (using dekiscript) and a lot of useful extensions that make it possible to mash-up all sorts of content. You can easily embed videos and RSS feeds, view PDF/DOC/XLS/PS/RTF documets, SVG images or interface with tweeter/linkedin/skype(?) etc. It is basically mediawiki on steroids! Not that all of this is needed for this website but providing a rich platform will give the Gromacs community much more flexibility in sharing knowledge and experience. Tutorial videos, RSS feeds to sites of interest, current weather in Stockholm, etc. can enrich the site by a lot. I would have approached this process differently. The MediaWiki content was intrinsically free-form, and now we're apparently trying to shoehorn it into something hierarchical. This process converts hundreds of links that are now defunct because they were created as relative links to targets in a free-form database, and have now been automatically converted to what look like hard links to non-existent targets. The correct targets are presumably placed somewhere in a fairly arbitrary hierarchy (e.g. what's the difference between Best Practices and How-tos?), which anyone wanting to spend the time to fix now has to memorise. These categories existed in the previous wiki, but nobody adding content or links was forced to use or know them. That's a big change in philosophy. In fact, dekiwiki can be very easily set up as a graph/free-form style wiki. One just has to disable the navigation pane, one click away. Then you have only one page from which you can access the rest of the site. Also, in a wiki way, if you try to access a non-existing page you are automatically presented with the editor to add new page to the top level. Hyperlinks to other pages on the site are also relative as in a standard wiki, so even if you rename a page or move it to a different level in the tree (if you are using one) all links pointing to it will be able to find it. I've spent a lot of time over years creating and maintaining a large slab of this content (with other notable contributions from quite a few people - Dallas Warren in particular) and feel that this new imported format greatly reduces the utility of the information. While some curated hierarchical indexes are good things for helping to find content, I think preserving the underlying lack of hierarchy is a much better approach to preserving the usefulness of the content. The alternative is appointing a curator and having them spend lots of time organizing and fixing links. Given the slow rate of transition of GROMACS web content from old to new forms, I think we should be very keen not to make more centralized work, and to preserve the goodwill of previous external volunteers :-) I can easily remove the left pane and leave only a flat graph structure if that's better. It wasn't easy to categories all the info from the previous site but there is some inherent hierarchy in the type of content we have on the site. It is possible to combine both styles. How about keeping the tree and put easily categorizable content into the appropriate level? Then, have a top level Others (or something like that) where you can dump any page that doesn't fit the structure, and include link to it from another place. Same would hold for levels like How-tos and Programming Guide. They can have 100s of sub-pages but you don't need to scroll down to find something. Put a new page there along with a link to it at some other page. Last but not least, there is a search form:) I'd much rather see the Documentation section (http://www.gromacs.org/Documentation) have links to * the paper manuals, * either a compatible Wiki, or a flat wiki-style import of the previous wiki (so that automated link conversion can just work - even if it's done with a simple perl script!), * some new and updated index pages for that previous wiki, * and if necessary, any other non-wiki content. Dear Mark, you raise many good points. A lot of the strong points of the simple wiki have been lost in the transition, I guess we have been misled by the wiki in the name Dekiwiki. Dekiwiki has some important advantages over mediawiki, like security (apparently the oldwiki was abused by spammers recently, this is why it was shutdown), and the ease for adding images and documents (mdp files :)). Whether dekiwki was the right choice for the job I am not sure. Overall it is easy to conclude that the move was done too hastily, seeing that the new website is still not anywhere close as informative as the two previous websites
[gmx-users] Mailing List Search on the new website
Hi, It is now possible to search the mailing list archives from the new website: http://www.gromacs.org/Support/Mailing_Lists/Search . There is a link to it at the Quick Links section on the front page also. Currently: * Only the [gmx-users] mailng list is being indexed. * The index is updated every 2 hours. * The search input is not parsed, rather search is done only for the exact string. * The results are displayed in descending order of the date. You can change the sorting by clicking on the column names. * For some postings, the contents section in the table is empty but following the link will display the full contents. * It is likely that the interface will be implemented into the website differently. Also, almost all of the information from the old wiki/www sites is now transfered and incorporated, although many pages contain broken links to them. They will be fixed one by one, but everyone is welcome to update them when you come across such. Rossen ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
