[gmx-users] installation error under openSuse 12.2
> Date: Mon, 11 Nov 2013 08:27:05 -0800 (PST) > From: kolnkempff > Subject: [gmx-users] installation error under openSuse 12.2 > To: gmx-users@gromacs.org > Message-ID: <1384187225465-5012430.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Dear gmx-users, > > I am trying to install gromacs-4.6.3 on an older Dell that is running > openSuse 12.2 > > Using "DGMX_BUILD_OWN_FFTW=ON" failed for me so to get through cmake I had > to compile fftw from scratch and I followed the recommendation of going > directly to their website. Now I am at the make stage and get the following > message: > > [ 67%] Built target gmxfftw > make[2]: *** No rule to make target > `//home/koln/bin/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', > needed by `src/gmxlib/libgmx.so.8'. Stop. > make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 > make: *** [all] Error 2 > > > When I check for libfftw, I get: > > koln@linux-5bim:~/bin/gromacs-4.6.3/build2> rpm -qf /usr/lib/libfftw3f.* > libfftw3-3-32bit-3.3.2-1.1.2.x86_64 > > Any suggestions for how to get past this obstacle would be greatly > appreciated! This is an known issue in OpenSuse! We added a workaround a while ago: https://gerrit.gromacs.org/#/c/2540/ Until Gromacs release 4.6.4. you will have to change line 41 of src/contrib/fftw/CMakeLists.txt yourself or just install fftw through OpenSuse or by hand. Christoph > > Koln > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/installation-error-under-openSuse-12-2-tp5012430.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Christoph Junghans Web: http://www.compphys.de -- 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: 'Command not found' after installation
> Date: Sun, 25 Aug 2013 14:31:51 -0700 (PDT)
> From: Nimmy McNimmerson
> Subject: Re: [gmx-users] 'Command not found' after installation
> To: Discussion list for GROMACS users
> Message-ID:
> <1377466311.57911.yahoomail...@web122305.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hmm... To be honest I'm a novice at installing complex things, I'm a computer
> scientist by trade but I'm not very good at troubleshooting this kind of
> thing. Has anyone actually installed GROMACS on mac and what did you do?
> (Using the default gcc/g++ doesn't work for the AVX stuff)
I got it working, but with gcc, only.
I would try the following:
1.) Find libiomp5.dylib
find / -iname libiomp5.dylib
2.) Update dyld search path by adding the directory from step 1
export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:/path/to/libiomp5"
to your .bashrc or GMXRC.bash
Christoph
>
>
>
> From: Mark Abraham
> To: Discussion list for GROMACS users
> Sent: Sunday, August 25, 2013 12:57 AM
> Subject: Re: [gmx-users] 'Command not found' after installation
>
>
> Hi,
>
> I don't have any experience with icc on Mac, but I would try either
> * re-reading the icc docs to see whether you should be source-ing some
> configuration file to set up the dynamic loading at run time (as well
> as at compile time), and/or
> * making a static build (cmake -DBUILD_SHARED_LIBS=off; but some
> Google hits suggests icc was broken at some point and iomp5 enforces
> dynamic linking, go figure!),
> * when you're really sure you've set up your build environment
> correctly, complaining at Intel (again) :-)
>
> Mark
>
> On Sun, Aug 25, 2013 at 7:18 AM, Nimmy McNimmerson wrote:
>> Hi,
>>
>> Apparently this is an issue with my intel compiler; the dynamic linker isn't
>> finding the libiomp5.dylib library. However, I don't know how to fix this
>> (the google results haven't worked.)
>>
>> Please help,
>>
>> Thanks,
>> John
>>
>>
>>
>> From: "Barnett, James W."
>> To:
>> Sent: Saturday, August 24, 2013 3:07 PM
>> Subject: Re: [gmx-users] 'Command not found' after installation
>>
>>
>> Unfortunately this is now beyond what I know with a Mac. It sounds like a
>> library is missing that GROMACS needs, or GROMACS can't find it, which is
>> probably a simple fix.
>>
>> Perhaps someone more familiar with Mac will be able to weigh in.
>>
>> jbarn...@tulane.edu | from mobile
>>
>> wrote:
>>
>>>This gives the following:
>>>
>>>dyld: Library not loaded: libiomp5.dylib
>>> Referenced from: /usr/local/gromacs/bin/g_luck
>>> Reason: image not found
>>>Trace/BPT trap: 5
>>>
>>>If I try 'pdb2gmx', it says:
>>>
>>>dyld: Library not loaded: libiomp5.dylib
>>> Referenced from: /usr/local/gromacs/bin/pdb2gmx
>>> Reason: image not found
>>>Trace/BPT trap: 5
>>>
>>>Did the installation not work properly?
>>>
>>>
>>>
>>> From: "Barnett, James W."
>>>To: Nimmy McNimmerson ; Discussion list for GROMACS
>>>users
>>>Sent: Saturday, August 24, 2013 10:42 AM
>>>Subject: Re: [gmx-users] 'Command not found' after installation
>>>
>>>
>>>Try "g_luck". That's what has worked for me.
>>>
>>>On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote:
>>>> Hello all,
>>>> I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I
>>>> downloaded the latest Intel C++ compilers and built Gromacs successfully
>>>> (at least it appeared to be successful since I saw no error messages). I
>>>> appended this line to my ~/.profile file: source
>>>> /usr/local/gromacs/bin/GMXRC.bash, and restarted my terminal. Still, every
>>>> time I type in a GROMACS command, such as "luck," it says "command not
>>>> found." f I do echo $GMXDATA, it does return
>>>> /usr/local/gromacs/share/gromacs, though.
>>>> Thanks,
>>>> John
>>>>
>>>
>>>
>>>--
>>>Wes Barnett | jbarn...@tulane.edu
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Suppo
[gmx-users] Re: Unable to download Gromacs source tar file
> Date: Sat, 8 Jun 2013 13:57:51 +0200 > From: Mark Abraham > Subject: Re: [gmx-users] Unable to download Gromacs source tar file > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > As a work-around, you can try to get archives from > https://github.com/gromacs/gromacs/tags (but these will not quite match the > official tarballs - but in ways that don't matter for simulating). > Or use google to find the tarball: <https://www.google.com/search?q=intitle:%22index+of%22+gromacs-4.6.1.tar.gz> Christoph > Mark > > > On Sat, Jun 8, 2013 at 1:54 PM, Mark Abraham wrote: > >> I just downloaded the 4.5.7 tarball to a machine in Australia. >> >> Mark >> >> >> On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury wrote: >> >>> I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). >>> >>> Chandan >>> >>> >>> -- >>> Chandan kumar Choudhury >>> NCL, Pune >>> INDIA >>> >>> >>> On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham >> >wrote: >>> >>> > They're still fine. There must be a problem at your end, I'm afraid. >>> > >>> > Mark >>> > >>> > >>> > On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy < >>> > bhamymait...@aero.iisc.ernet.in> wrote: >>> > >>> > > >>> > > Hi, >>> > > Thanks for your reply. But the problem still persists. Even now I am >>> not >>> > > able to download. >>> > > >>> > > -Original Message- >>> > > From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham >>> > > Sent: Fri 6/7/2013 8:14 PM >>> > > To: Discussion list for GROMACS users >>> > > Subject: Re: [gmx-users] Unable to download Gromacs source tar file >>> > > >>> > > They're fine now. Perhaps the FTP server was offline briefly. >>> > > >>> > > Mark >>> > > >>> > > >>> > > On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy < >>> > > bhamymait...@aero.iisc.ernet.in> wrote: >>> > > >>> > > > >>> > > > Hi, >>> > > > I would like to use Gromacs for MD simulation of biomolecules. But >>> I am >>> > > > not able to download any of the source files from the link >>> > > > http://www.gromacs.org/Downloads >>> > > > >>> > > > Can anyone please help. >>> > > > Thanks and regards, >>> > > > Maithry >>> > > > >>> > > > -- >>> > > > This message has been scanned for viruses and >>> > > > dangerous content by MailScanner, and is >>> > > > believed to be clean. >>> > > > >>> > > > -- >>> > > > 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 >>> > > >>> > > -- >>> > > This message has been scanned for viruses and >>> > > dangerous content by MailScanner, and is >>> > > believed to be clean. >>> > > >>> > > >>> > > >>> > > >>> > > -- >>> > > This message has been scanned for viruses and >>> > > dangerous content by MailScanner, and is >>> &g
[gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER
> Date: Wed, 08 May 2013 16:34:46 +0200
> From: Julian Garrec
> Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
> vs AMBER
> To: Discussion list for GROMACS users
> Message-ID: <518a6286.8020...@epfl.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> No suggestion ?? :)
>
> In my post I forgot to say that my system contains explicit water.
>
> I'm still very curious about the difference in implementation in AMBER
> and GROMACS. And I still don't really understand the meanning of tau-t
> in LD and how it is related to other (well defined) quantities such as
> the friction coeficient in equation 3.114 of the manual (v4.6.1).
I am not really sure what your question is, section 7.3.3 is pretty
clear about that:
"the inverse friction constant for each group is set with tau-t", so
gamma_i=1/tau-t, which also makes sense unit-wise as gamma has units
1/ps and tau-t ps
bd-fric is only used for the Brownian dynamics integrator and if
bd-fric=0, the friction is calculated as mass/tau-t. It might be a bit
misleading that bd-fric is listed under section 7.3.4 (Langevin
dynamics), but that stems from the fact that Brownian dynamics is the
overdamped case of stochastic dynamics and hence it is Langevin
Dynamics, too, just in a different limit.
Christoph
>
> Please help,
>
> Sincerely,
>
> Julian
>
>
> Le 04/05/13 13:42, Julian Garrec a 閏rit :
>> Dear all,
>>
>> I am trying to use stochastic dynamics in GROMACS to reproduce some
>> previous results that I got with the AMBER software using the Langevin
>> thermostat.
>>
>> In AMBER, one typically sets what they call the "collision frequency"
>> (noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2
>> collisions per ps (significantly smaller than the internal friction of
>> water, since I use Langevin dynamics as a thermostat).
>>
>> 1) In the mdp options manual, it is recommended to use {integrator=sd
>> ; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds
>> to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the
>> manual (version 4.6.1). Am I right ?
>>
>> 2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to
>> {integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the
>> manual, it is said that gamma_i should be set to 0.5 to follow the
>> same spirit).
>>
>> 3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?
>>
>> Thanks for your help,
>>
>> Julian
>>
>
>
> --
> Julian Garrec, research associate
>
> Web: https://sites.google.com/site/juliangarrec/
>
> 蓂uipe : Chimie et Biochimie Th閛riques
> Unit�Mixte de Recherches CNRS UHP 7565
> Universit�de Lorraine, Nancy I BP 239,
> 54506 Vandoeuvre-l鑣-Nancy, cedex France
--
Christoph Junghans
Web: http://www.compphys.de
--
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[gmx-users] Re: installation Gromacs-Fedora18
types.h... yes >> > checking for stdint.h... yes >> > checking for unistd.h... yes >> > checking for unistd.h... (cached) yes >> > checking sys/time.h usability... yes >> > checking sys/time.h presence... yes >> > checking for sys/time.h... yes >> > checking sched.h usability... yes >> > checking sched.h presence... yes >> > checking for sched.h... yes >> > checking for sysconf... yes >> > checking for the pthreads library -lpthreads... no >> > checking whether pthreads work without any flags... no >> > checking whether pthreads work with -Kthread... no >> > checking whether pthreads work with -kthread... no >> > checking for the pthreads library -llthread... no >> > checking whether pthreads work with -pthread... yes >> > checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE >> > checking if more special flags are required for pthreads... no >> > checking for cc_r... cc >> > checking if atomic operations are supported... yes >> > checking if pthread_setaffinity_np is available... yes >> > checking whether byte ordering is bigendian... no >> > checking that size_t can hold pointers... yes >> > checking for SIGUSR1... yes >> > checking for pipes... yes >> > checking floating-point format... IEEE754 (little-endian byte and word >> > order) >> > checking whether ln -s works... yes >> > checking whether make sets $(MAKE)... (cached) yes >> > checking for a sed that does not truncate output... /usr/bin/sed >> > checking for ld used by cc ... /usr/bin/ld >> > checking if the linker (/usr/bin/ld) is GNU ld... yes >> > checking for /usr/bin/ld option to reload object files... -r >> > checking for BSD-compatible nm... /usr/bin/nm -B >> > checking how to recognise dependent libraries... pass_all >> > checking dlfcn.h usability... yes >> > checking dlfcn.h presence... yes >> > checking for dlfcn.h... yes >> > checking for g++... g++ >> > checking whether we are using the GNU C++ compiler... yes >> > checking whether g++ accepts -g... yes >> > checking dependency style of g++... gcc3 >> > checking how to run the C++ preprocessor... g++ -E >> > checking the maximum length of command line arguments... 32768 >> > checking command to parse /usr/bin/nm -B output from cc object... ok >> > checking for objdir... .libs >> > checking for ar... ar >> > checking for ranlib... ranlib >> > checking for strip... strip >> > checking if cc supports -fno-rtti -fno-exceptions... no >> > checking for cc option to produce PIC... -fPIC >> > checking if cc PIC flag -fPIC works... yes >> > checking if cc static flag -static works... no >> > checking if cc supports -c -o file.o... yes >> > checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports >> > shared >> > libraries... yes >> > checking whether -lc should be explicitly linked in... no >> > checking dynamic linker characteristics... GNU/Linux ld.so >> > checking how to hardcode library paths into programs... immediate >> > checking whether stripping libraries is possible... yes >> > checking for shl_load... no >> > checking for shl_load in -ldld... no >> > checking for dlopen... no >> > checking for dlopen in -ldl... yes >> > checking whether a program can dlopen itself... yes >> > checking whether a statically linked program can dlopen itself... yes >> > checking if libtool supports shared libraries... yes >> > checking whether to build shared libraries... yes >> > checking whether to build static libraries... yes >> > configure: creating libtool >> > appending configuration tag "CXX" to libtool >> > checking for ld used by g++... /usr/bin/ld -m elf_x86_64 >> > checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes >> > checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports >> > shared >> > libraries... yes >> > checking for g++ option to produce PIC... -fPIC >> > checking if g++ PIC flag -fPIC works... yes >> > checking if g++ static flag -static works... no >> > checking if g++ supports -c -o file.o... yes >> > checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports >> > shared >> > libraries... yes >> > checking dynamic linker characteristics... GNU/Linux ld.so >> > checking how to hardcode library paths into programs... immediate >>
[gmx-users] Re: Manual installation of new analysis tool
`pbc_rvec_sub':* >> *distances.c:(.text+0x4e8): undefined reference to `pbc_dx'* >> *distances.o: In function `get_distance':* >> *distances.c:(.text+0x550): undefined reference to `sqrtf'* >> *distances.o: In function `center_of_mass':* >> *distances.c:(.text+0x6b5): undefined reference to `save_calloc'* >> *dist_mode.o: In function `gmx_log2':* >> *dist_mode.c:(.text+0xa8): undefined reference to `log'* >> *dist_mode.o: In function `gmx_invsqrt':* >> *dist_mode.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* >> *dist_mode.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'* >> *dist_mode.o: In function `norm':* >> *dist_mode.c:(.text+0x1fc): undefined reference to `sqrt'* >> *dist_mode.o: In function `matrix_convert':* >> *dist_mode.c:(.text+0x2fa): undefined reference to `cos'* >> *dist_mode.c:(.text+0x326): undefined reference to `sin'* >> *dist_mode.c:(.text+0x353): undefined reference to `cos'* >> *dist_mode.c:(.text+0x37c): undefined reference to `cos'* >> *dist_mode.c:(.text+0x38f): undefined reference to `cos'* >> *dist_mode.c:(.text+0x3a2): undefined reference to `cos'* >> *dist_mode.c:(.text+0x3c0): undefined reference to `sin'* >> *dist_mode.c:(.text+0x414): undefined reference to `sqrt'* >> *dist_mode.o: In function `_min_distance':* >> *dist_mode.c:(.text+0x505): undefined reference to `pbc_dx'* >> *dist_mode.o: In function `build_dist':* >> *dist_mode.c:(.text+0x5af): undefined reference to `save_calloc'* >> *dist_mode.c:(.text+0x65c): undefined reference to `save_calloc'* >> *dist_mode.c:(.text+0x6a3): undefined reference to `save_calloc'* >> *dist_mode.c:(.text+0x710): undefined reference to `save_calloc'* >> *dist_mode.c:(.text+0x73f): undefined reference to `save_calloc'* >> *dist_mode.o:dist_mode.c:(.text+0x76e): more undefined references to >> `save_calloc' follow* >> *dist_mode.o: In function `build_dist':* >> *dist_mode.c:(.text+0x7b2): undefined reference to `get_index'* >> *dist_mode.c:(.text+0x839): undefined reference to `xvgropen'* >> *dist_mode.c:(.text+0x865): undefined reference to `xvgr_legend'* >> *dist_mode.o: In function `clean_dist':* >> *dist_mode.c:(.text+0x8bd): undefined reference to `save_free'* >> *dist_mode.c:(.text+0x8f1): undefined reference to `save_free'* >> *dist_mode.c:(.text+0x917): undefined reference to `save_free'* >> *dist_mode.c:(.text+0x948): undefined reference to `save_free'* >> *grid_mode.o: In function `build_grids':* >> *grid_mode.c:(.text+0x81): undefined reference to `save_calloc'* >> *grid_mode.c:(.text+0x177): undefined reference to `gmx_fatal'* >> *grid_mode.c:(.text+0x1a2): undefined reference to `save_calloc'* >> *grid_mode.c:(.text+0x201): undefined reference to `ffopen'* >> *grid_mode.o: In function `clean_grids':* >> *grid_mode.c:(.text+0x2b8): undefined reference to `save_free'* >> *grid_mode.c:(.text+0x2c6): undefined reference to `ffclose'* >> *grid_mode.c:(.text+0x2e9): undefined reference to `save_free'* >> *grid_mode.o: In function `grid_store':* >> *grid_mode.c:(.text+0x41a): undefined reference to `put_atom_in_box'* >> *collect2: ld returned 1 exit status* >> *make: *** [g_mydensity] Error 1* >> >> Please help me in this regard. Thanks for your valuable time and concern. >> >> -- >> With Best Wishes >> Venkat Reddy Chirasani >> PhD student >> Laboratory of Computational Biophysics >> Department of Biotechnology >> IIT Madras >> Chennai >> INDIA-600036 >> -- >> 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 >> > > -- Christoph Junghans Web: http://www.compphys.de -- 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: compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition
Virginia Tech >> > > > Blacksburg, VA >> > > > jalemkul[at]vt.edu | (540) 231-9080 >> > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > > > >> > > > ==**== >> > > > -- >> > > > gmx-users mailing listgmx-users@gromacs.org >> > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > > > * Please search the archive at http://www.gromacs.org/** >> > > > Support/Mailing_Lists/Search< >> > > 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< >> > > http://www.gromacs.org/Support/Mailing_Lists> >> > > > >> > > >> > > >> > > >> > > -- >> > > Best Regards, >> > > >> > > Qinghua >> > > -- >> > > 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 >> > > >> > >> > >> > >> > -- >> > Ahmet Yıldırım >> > -- >> > 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 >> > >> >> >> >> -- >> Best Regards, >> >> Qinghua >> -- >> 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 list > gmx-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! > > End of gmx-users Digest, Vol 107, Issue 116 > *** -- Christoph Junghans Web: http://www.compphys.de -- 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: gromacs VERSION 4.0.7-There is no domain
> Date: Sun, 10 Mar 2013 03:17:24 -0700 (PDT) > From: Hamid Mosaddeghi > Subject: [gmx-users] Re: gromacs VERSION 4.0.7-There is no domain > decomposition. > To: gmx-users@gromacs.org > Message-ID: <1362910644976-5006251.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Dear Christoph > > thanks for quick reply > >>It seems like mdrun was not able to find a decomposition >>automatically, try to give one by hand: >>$ mdrun -dd 2 2 4 > > this command is general or not? No, it is not general, but you wanted to run on 16 cores, so a decomposition of 2x2x4 (=16 and 4 in z as the box was the longest in z) would work. > >>Btw, your gromacs is 2 major versions behind, it might be a good idea to > update > > yes, but I modify some force field in this versiom nad need to work with it If this change is of general interest, create a patch and submit it here: <https://gerrit.gromacs.org/> > > > do you think I go to new version, don't get this error? Many many things has been improved from 4.0 to 4.6, so I think it is save to say it will most likely work. > > Best Regards > > Hamid Mosaddeghi > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Re-gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006247p5006251.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > -- > > -- > gmx-users mailing list > gmx-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! > > End of gmx-users Digest, Vol 107, Issue 42 > ** -- Christoph Junghans Web: http://www.compphys.de -- 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: gromacs VERSION 4.0.7-There is no domain decomposition.....
Dear Hamid, please post these kind of questions on the users and not the developers list. 2013/3/9 Hamid Mosaddeghi : > Dear users > > I used gromacs for my system include CNT-water-ion-protein (400,000atom), I > used grompp without error. > > after used mdrun with 16 node on cluster, I get this error: > > Reading file nvt.tpr, VERSION 4.0.7 (single precision) > Loaded with Money > > > NOTE: Periodic molecules: can not easily determine the required minimum > bonded cut-off, using half the non-bonded cut-off > > > Will use 15 particle-particle and 1 PME only nodes > This is a guess, check the performance at the end of the log file > > --- > Program mdrun, VERSION 4.0.7 > Source code file: domdec.c, line: 5888 > > Fatal error: > There is no domain decomposition for 15 nodes that is compatible with the > given box and a minimum cell size of 3.75 nm > Change the number of nodes or mdrun option -rdd or -dds > Look in the log file for details on the domain decomposition > --- > > "Good Music Saves your Soul" (Lemmy) > > Error on node 0, will try to stop all the nodes > Halting parallel program mdrun on CPU 0 out of 16 > > --- > > my box size is 14*14*18. > > I used mdrun -rdd 1 , gromacs run without error is it correct or not? If you are sure that the maximum distance of your bonded interactions is 1nm, you can do that. It seems like mdrun was not able to find a decomposition automatically, try to give one by hand: $ mdrun -dd 2 2 4 Btw, your gromacs is 2 major versions behind, it might be a good idea to update. Christoph > > I get this error in NVT (Em run without error). > > Best Regards. > > Hamid Mosaddeghi > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006246.html > Sent from the GROMACS Developers Forum mailing list archive at Nabble.com. > -- > gmx-developers mailing list > gmx-develop...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-developers > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-developers-requ...@gromacs.org. -- Christoph Junghans Web: http://www.compphys.de -- 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] Gromacs 4.6.1 ATLAS/CUDA detection problems...
2013/3/6 Evren Yurtesen IB : > Hi Christoph, > > I thought problems in the compilation is more related to devs than users. > But I sure can send mail first to users list in future. Thanks. > > I used the following to get it working. > > mkdir build_cmake > cd build_cmake > cmake .. -DCMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2 > > This does not seem to work > > mkdir build_cmake > cd build_cmake > export CMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2 > cmake .. > > Was this the information you were looking for? That looks ok. I had a another look at the issue and I guess cmake's blas detention is a bit flaky, when it comes to static libraries. You are using liblapack.a, which has no link information, with liblapack.so it should have worked. Anyhow, thanks for reporting the issue. Christoph > > Thanks > Evren > > > > > On Wed, 6 Mar 2013, Christoph Junghans wrote: > >> Hi Evren, >> >> please post these kind of questions on the users list as they are not >> really related to the development of gromacs. >> >> Concerning your question below, can you please post your cmake >> configure command line? >> >> Christoph >> >> 2013/3/6 Evren Yurtesen IB : >>> >>> Sorry for the double post. I tried to post it from web and it said the >>> post >>> was not accepted to mailing list but then it arrived anyway. >>> >>> In addition the manual mentions setting CMAKE_INSTALL_PREFIX however this >>> does not work when it is "set" it only works when given to cmake as a >>> parameter with -DCMAKE_INSTALL_PREFIX=/something >>> >>> http://www.gromacs.org/Documentation/Installation_Instructions#4.3._CMake_advanced_options >>> >>> When I do an 'export CMAKE_INSTALL_PREFIX=/something' this is does not >>> seem >>> to propagate to configuration files, interestingly 'export >>> CMAKE_PREFIX_PATH=/libpaths' seem to have the desired effect. >>> >>> Thanks, >>> Evren >>> >>> >>> On Wed, 6 Mar 2013, Evren Yurtesen IB wrote: >>> >>>> Hello, >>>> >>>> I am not exactly sure if this is a bug but I realized that cmake system >>>> of >>>> gromacs couldnt find my ATLAS libraries. First problem was that it >>>> needed >>>> -lgfortran (and then -lcblas also) for compiling with gcc. The error I >>>> found >>>> in cmake error file can be found below. >>>> >>>> In addition while documentation suggests latest GCC versions, the only >>>> compatible version of GCC with CUDA 5.0 is GCC 4.6 but there doesnt seem >>>> to >>>> be any checks for this. >>>> >>>> Run Build Command:/usr/bin/gmake "cmTryCompileExec3752895534/fast" >>>> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3752895534.dir/build.make >>>> CMakeFiles/cmTryCompileExec3752895534.dir/build >>>> gmake[1]: Entering directory >>>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' >>>> /usr/bin/cmake -E cmake_progress_report >>>> >>>> /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles >>>> 1 >>>> Building C object >>>> CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o >>>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra >>>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused >>>> -Wunused-value -march=native -mtune=native >>>> -DCHECK_FUNCTION_EXISTS=dgemm_ >>>> -o CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o >>>> -c >>>> /usr/share/cmake/Modules/CheckFunctionExists.c >>>> Linking C executable cmTryCompileExec3752895534 >>>> /usr/bin/cmake -E cmake_link_script >>>> CMakeFiles/cmTryCompileExec3752895534.dir/link.txt --verbose=1 >>>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra >>>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused >>>> -Wunused-value -march=native -mtune=native >>>> -DCHECK_FUNCTION_EXISTS=dgemm_ >>>> CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o -o >>>> cmTryCompileExec3752895534 -rdynamic -Wl,-Bstatic -lf77blas -latlas >>>> -Wl,-Bdynamic >>>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/libf77blas.a(xerbla.o): In >>>> function `xerbla_': >>>>
[gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
nce to `cblas_cgemm' >> ATL_larfb.c:(.text+0x1ccf): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x1d3c): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x1d95): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x1e09): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x1e8e): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x1ee6): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x1f4e): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x1fa7): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x201c): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x20b0): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x2108): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x2170): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x21c9): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x2240): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x22dc): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x2333): undefined reference to `cblas_ctrmm' >> ATL_larfb.c:(.text+0x23a0): undefined reference to `cblas_cgemm' >> ATL_larfb.c:(.text+0x23f9): undefined reference to `cblas_ctrmm' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarft_blockFC': >> ATL_larft.c:(.text+0x152): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x1c3): undefined reference to `cblas_cgemm' >> ATL_larft.c:(.text+0x211): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x254): undefined reference to `cblas_ctrmm' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarft_blockFR': >> ATL_larft.c:(.text+0x3bd): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x433): undefined reference to `cblas_cgemm' >> ATL_larft.c:(.text+0x481): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x4c4): undefined reference to `cblas_ctrmm' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarft_blockBC': >> ATL_larft.c:(.text+0x643): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x69d): undefined reference to `cblas_cgemm' >> ATL_larft.c:(.text+0x6e8): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x72e): undefined reference to `cblas_ctrmm' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarft_blockBR': >> ATL_larft.c:(.text+0x8c8): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x920): undefined reference to `cblas_cgemm' >> ATL_larft.c:(.text+0x96b): undefined reference to `cblas_ctrmm' >> ATL_larft.c:(.text+0x9b1): undefined reference to `cblas_ctrmm' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarftFC': >> ATL_larft.c:(.text+0xcfb): undefined reference to `cblas_cdotc_sub' >> ATL_larft.c:(.text+0xdb3): undefined reference to `cblas_cdotu_sub' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarftBC': >> ATL_larft.c:(.text+0xffd): undefined reference to `cblas_cdotc_sub' >> ATL_larft.c:(.text+0x10a9): undefined reference to `cblas_cdotu_sub' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarftFR': >> ATL_larft.c:(.text+0x1368): undefined reference to `cblas_cdotc_sub' >> ATL_larft.c:(.text+0x1422): undefined reference to `cblas_cdotu_sub' >> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In >> function `ATL_clarftBR': >> ATL_larft.c:(.text+0x165d): undefined reference to `cblas_cdotc_sub' >> ATL_larft.c:(.text+0x1713): undefined reference to `cblas_cdotu_sub' >> collect2: error: ld returned 1 exit status >> gmake[1]: *** [cmTryCompileExec2027137673] Error 1 >> gmake[1]: Leaving directory >> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' >> gmake: *** [cmTryCompileExec2027137673/fast] Error 2 >> >> >> >> Thanks, >> Evren >> -- >> gmx-developers mailing list >> gmx-develop...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-developers >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-developers-requ...@gromacs.org. >> > -- > gmx-developers mailing list > gmx-develop...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-developers > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-developers-requ...@gromacs.org. -- Christoph Junghans Web: http://www.compphys.de -- 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: gInstallation Problems with Gromacs4.6
> Date: Fri, 1 Mar 2013 23:59:36 +0530
> From: "Abhishek Acharya"
> Subject: [gmx-users] Installation Problems with Gromacs4.6
> To: "gromacs maillist"
> Message-ID:
> <2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello Gromacs Users.
> I have been trying to install Gromacs4.6 on our HPC facility. I think I
> have correctly provided all the necessary mpi and fftw library paths. But
> when i try to run configure it gives me the following error:
>
> CMake Error at cmake/FindFFTW.cmake:105 (message):
>Could not find fftwf_plan_r2r_1d in
>/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
>error message in
>/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
>find out what went wrong. If you are using a static lib (.a) make sure
> you
>have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
> Call Stack (most recent call first):
>CMakeLists.txt:894 (find_package)
>
> As suggested here I looked into the CMakeError.log file of which I can't
> make any sense.
>
> Source file was:
> #include
> int main(void) {
> void* buf;
> MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
> }
> Determining if the function fftwf_plan_r2r_1d exists in the
> /home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
> Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
>
> Run Build Command:/usr/bin/gmake "cmTryCompileExec2668319475/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
> CMakeFiles/cmTryCompileExec2668319475.dir/build
> gmake[1]: Entering directory
> `/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
> /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
> /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
> 1
> Building C object
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
> /usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
> -Wall -Wno-unused -Wunused-value
> -DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
> /home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
> Linking C executable cmTryCompileExec2668319475
> /home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
> CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
> /usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
> -Wall -Wno-unused -Wunused-value
> -DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
> -L/home/aacharya/softwares/fftw-3.3.3/lib
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
> cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a "-lfftw3f" before "-lm". Can you
tell us what your cmake command line was?
> CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
> function `main':
> CheckFunctionExists.c:(.text+0x15): undefined reference to
> `fftwf_plan_r2r_1d'
> collect2: ld returned 1 exit status
> gmake[1]: *** [cmTryCompileExec2668319475] Error 1
> gmake[1]: Leaving directory
> `/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec2668319475/fast] Error 2
>
>
> Kindly help. I tried installing 4.5.6 and it got installed without any
> such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
> and I am using the Verlet cutoff scheme.
> Thanks in advance
> With Regards
> Abhishek Acharya
--
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[gmx-users] Re: gmx-users Digest, Vol 106, Issue 69
> Date: Wed, 13 Feb 2013 16:07:53 + > From: Steven Neumann > Subject: [gmx-users] Bond potential of atom groups > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Gmx Users, > > I want to create coarse grained model. I need bond constant and > equilibrium distance according to the equation > > V(r) =K (R - Req)^2 > > I wish to extract bonded potential between beads made out 3 atoms. I > need Req and K. Equilibrium distance is straight forward - g_dist > between COM or COG with index file conatining those 3 atoms. To match > force constant K I need to extract bonded potential and try to fit to > my parabolic curve. > > My question: > > How can I get bonded potential between beads of 3 atoms from AA > simulation? Do I have to specify energy groups (energgrps) before the > run in my mdp and then use g_energy? Have a look at the hexane example in the tutorials of the VOTCA package: <https://code.google.com/p/votca/source/browse/?repo=csg-tutorials#hg%2Fhexane%2Fatomistic> You will have to modify the mapping file (hexane.xml) a bit for your case, after that you can use the csg_boltzmann program to calculate the potential from the mapped distribution and try to fit the resulting potential table with the above mentioned functional form. (The VOTCA manual gives more details about these steps.) If you have further questions contact the VOTCA mailing list: vo...@googlegroups.com Cheers, Christoph > > Thank you > > Steven -- Christoph Junghans Web: http://www.compphys.de -- 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: gromacs-4.6.tar.gz installation question
> Date: Mon, 04 Feb 2013 15:32:17 -0500 > From: Justin Lemkul > Subject: Re: [gmx-users] gromacs-4.6.tar.gz installation question > To: Discussion list for GROMACS users > Message-ID: <51101ad1.3000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 2/4/13 3:30 PM, jeela keel wrote: >> *Dear All, >> >> I am trying to install gromacs, I dowloaded >> **gromacs-4.6.tar.gz<ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz>and >> following the instruction in the following website >> http://www.gromacs.org/Documentation/Installation_Instructions#4._Doing_a_build_of_GROMACS >> >> I read the instraction but I am still kind of confused. Do I need to >> download both FFTW and CMake or just choose one of them for the gromacs >> installation? > > Both. FFTW is used for Fourier transforms. CMake is the compiler that builds > the software. > >> Also can I use FTTW >> **fftw-2.1.5.tar.gz<ftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gz>instead >> of >> **fftw-3.3.3.tar.gz <ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3.tar.gz> becuase >> I also want to download Lammps in my computer that can only use fftw 2.1.5 >> > > We always advise using the newest version. There is no problem at all in > maintaining different versions in different locations. In Gromacs-4.6 we have dropped support for fftw-2, which is legacy for nearly 13 years now, so you will need to install fftw-3 and btw. lammps supports fftw3 since Aug 2011. An alternative is to use gromacs build-in fftw (GMX_BUILD_OWN_FFTW=ON). Christoph > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- Christoph Junghans Web: http://www.compphys.de -- 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: question about fftw3 in gromacs 4.6 installation
> Date: Fri, 01 Feb 2013 19:00:02 -0500
> From: Justin Lemkul
> Subject: Re: [gmx-users] Re: question about fftw3 in gromacs 4.6
> installation
> To: Discussion list for GROMACS users
> Message-ID: <510c5702.5080...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 2/1/13 5:26 PM, didymos wrote:
>> Hi Justin!
>>
>> I had the same problem and I used your advise but I am not sure if this
>> entirely worked for me...
>>
>> I used:
>> cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs
>> -DFFTWF_INCLUDE_DIR=$HOME/fftw/include
>> -DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so -DCMAKE_PREFIX_PATH=$HOME/fftw/
>> ..
>>
>
> The use of -DCMAKE_PREFIX_PATH eliminates the need for -DFFTWF_INCLUDE_DIR and
> -DFFTWF_LIBRARY. Not that this is the source of your problem, but you can
> certainly trim down your command.
>
>> and I got:
>> -- checking for module 'fftw3f'
>> -- found fftw3f, version 3.2.2
>> -- Looking for fftwf_plan_r2r_1d in
>> /home/users/didymos/fftw/lib/libfftw3f.so
>> -- Looking for fftwf_plan_r2r_1d in
>> /home/users/didymos/fftw/lib/libfftw3f.so - found
>> -- Looking for fftwf_have_simd_avx in
>> /home/users/didymos/fftw/lib/libfftw3f.so
>> -- Looking for fftwf_have_simd_avx in
>> /home/users/didymos/fftw/lib/libfftw3f.so - not found
>> -- Looking for fftwf_have_simd_sse2 in
>> /home/users/didymos/fftw/lib/libfftw3f.so
>> -- Looking for fftwf_have_simd_sse2 in
>> /home/users/didymos/fftw/lib/libfftw3f.so - found
>>
>> So it seems ok but I am not sure about first two lines:
>> -- checking for module 'fftw3f'
>> -- found fftw3f, version 3.2.2
>> it should be 3.3.3
>
> Is there a different FFTW installed anywhere else on your system? I believe
> the
> first "found fftw3f" statement comes from pkgconfig detection, but this is
> superseded by what you specify manually. Perhaps someone who is more familiar
> with this element of the build system can comment.
Justin is 100% right, -DFFTWF_{INCLUDE_DIR,LIBRARY} supersedes,
whatever pkg-config finds before, you can see which library is used in
the output, in your case /home/users/didymos/fftw/lib/libfftw3f.so is
used.
One can also tweak the pkg-config's detection by including
/home/users/didymos/fftw in its search path:
export PKG_CONFIG_PATH="$HOME/fftw/lib/pkgconfig"
and test if it works by
$ pkg-config --libs fftw3f
(I should add this trick to the wiki as setting PKG_CONFIG_PATH helps
to tweak the detection of fftw and gsl (when installed in same custom
location) with one variable.)
Christoph
>
> -Justin
>
> --
> ====
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
>
--
Christoph Junghans
Web: http://www.compphys.de
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
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Re: Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian
> Date: Thu, 24 Jan 2013 15:55:13 +0100 > From: Szil?rd P?ll > Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on > Debian > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Let me add two more things. > > Note that we *always* compare performance and acceleration to our > super-tuned state-of-the-art CPU code, which I can confidently say that is > among the fastest if not the fastest to date, and never to some slow (CPU) > implementation. Therefore, while other codes might be able to get 10-20x > with GPUs and many x-es even with pre-Fermi (CC <2.0) cards, for obvious > reasons we simply can't. Always check the following 10 points before believing the speed-up of any code: <http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html> And Gromacs does a pretty fair comparison. > > Still you'll get high *absolute performance* regardless whether you can use > CPU only or CPU+GPU, so this should be a decent deal, right? > > If anybody volunteers to add software-based floating point atomic > operations for CC <2.0 and try running the current kernels on earlier > hardware, I'm willing to give pointers, but I simply had no time to try it > myself. This would enable using earlier cards, with a considerable > performance penalty of emulated atomic ops (plus these cards are anyway > slower), but it *might* be worth a try! > > Feel free to drop me a mail if anybody is interested. > > Cheers, > > -- > Szilárd > > > On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll wrote: > >> On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul wrote: >> >>> >>> >>> On 1/24/13 9:23 AM, James Starlight wrote: >>> >>>> oh that was simply solved by upgrading of G++ :) >>>> >>>> the only problem which remains is the missing of support of mu GPU :( >>>> That time I've tried to start simulation on simply 2 cores CPU + geforce >>>> 9500 >>>> >>>> From md run I've obtained >>>>> >>>> >>>> NOTE: Error occurred during GPU detection: >>>>CUDA driver version is insufficient for CUDA runtime version >>>>Can not use GPU acceleration, will fall back to CPU kernels. >>>> >>>> ED sampling will be performed! >>>> ED: Reading edi file new_a2a_pca_biased.edi >>>> ED: Note: Reference and average structure are composed of the same atom >>>> indices. >>>> ED: Found 1 ED group. >>>> Using 1 MPI thread >>>> Using 2 OpenMP threads >>>> >>>> No GPUs detected >>>> >>>> >>>> I've installed cuda-5.0 with driver >>>> NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29 >>>> 00:05:49 PDT 2012 >>>> >>>> that system works fine with the recent nvidia GPU's but has no support >>>> for GeForce 9500. >>>> >>>> >>> GeForce 9500 cards have a compute capability of 1.1. The minimum >>> required for Gromacs is 2.0 (noted in the installation instructions). >> >> >> Exactly! Anything below CC 2.0 lacks certain features that make those >> devices rather slow for our algorithms and therefore pretty much >> impractical. >> >> Cheers, >> -- >> Szilárd >> >> >> >> >> >>> >>> >>> -Justin >>> >>> -- >>> ==**== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> >>> ==**== >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >> > > > -- > > -- > gmx-users mailing list > gmx-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! > > End of gmx-users Digest, Vol 105, Issue 119 > *** -- Christoph Junghans Web: http://www.compphys.de -- 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 with gromacs-4.6 compilation on Debian
> Date: Thu, 24 Jan 2013 01:07:04 +0100 > From: Szil?rd P?ll > Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on > Debian > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > Let me clarify one thing: I highly doubt that the *gcc version* upgrade is > what fixes your the issue, but rather the standard C++ library's version, > as you can see the undefined symbols refer to "GLIBCXX_3.4.15". Usually that is the case but for std::, the symbols are defined in libstdc++, which is part of the gcc package. $ strings /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libstdc++.so | grep _M_hook _ZNSt6__norm15_List_node_base7_M_hookEPS0_ _ZNSt15_List_node_base7_M_hookEPS_ _ZNSt8__detail15_List_node_base7_M_hookEPS0_ _ZNSt9__cxx199815_List_node_base7_M_hookEPS0_ Christoph > > Of course, updating the compiler is a perfectly fine solution if you get > the new (enough version of the) standard C++ library by doing so. > > Just wanted to clarify this for users bumping into this issue later. > > Cheers, > > -- > Szilárd -- Christoph Junghans Web: http://www.compphys.de -- 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 with gromacs-4.6 compilation on Debian
> Message: 5 > Date: Tue, 22 Jan 2013 19:42:01 +0100 > From: Szil?rd P?ll > Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on > Debian > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > On Tue, Jan 22, 2013 at 12:45 PM, James Starlight > wrote: > >> Szilárd, >> >> Today I've tried to re-install cuda+gromacs and do apt-get >> distr-upgrade but the same error was obtained during gromacs >> > > I'm don't see how does the distribution upgrade relate to the issues you > had (except if you have updated glibs to a newer version which is *still* > incompatible with libcuda. You should probably try getting a more recent > glibc and GCC version, one that libcuda is linked against. However, I'm not > sure what the source of your problem is, so I can't suggest a certain > solution. I had a similar problem on Gentoo Linux (https://bugs.gentoo.org/show_bug.cgi?id=452386), it helped to use a newer version of gcc (>=4.6). Cheers, Christoph > >> compilation. By the way where I could provide --add-needed option ? > > CMAKE_EXE_LINKER_FLAGS=-wl,--add-needed > > Cheers, > Szilárd > > >> >> >> James >> >> >> 2013/1/21 Szilárd Páll : >> > Szilárd >> -- >> 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 >> -- Christoph Junghans Web: http://www.compphys.de -- 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
