Hello gmx users!
As announced in my previous message at the beginning of the week, we
will be activating the new discussion forum today.
At the same time, the mailing list will move to read-only mode, so
please don't be surprised when it is no longer possible to submit new
messages to it.
Hello again @ all gmx-users!
A month has passed and we have moved forward with our work to move the
user mailing list to the [discussion forum]
https://gromacs.bioexcel.eu/. The discussion forum will open Friday, 8
May 2020.
We are now ready to accept people signing up to the forum at
Hi GROMACS users,
The official release of GROMACS 2020.2 is available!
This second patch release again fixes issues found since the initial
release of GROMACS 2020 and the release of 2020.1. We encourage all
users of the 2020
series to update to 2020.2. Please see the link to the release
Hello I am in search of a gromacs tutor to assist me with protein ion
channel dynamic simulations towards drug discovery, accordingly interested
parties please email for more details, thanks:)
--
Gromacs Users mailing list
* Please search the archive at
mx-users-boun...@maillist.sys.kth.se
on behalf of Szilárd Páll
Sent: Friday, April 24, 2020 6:06 PM
To: Discussion list for GROMACS users
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node
Hi,
Affinity settings on the Talos I
2 5275
> >
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Netaly
> > Khazanov
> > Sent: Sunday, April 26, 2020 15:38
> > To: Discussion list
_
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Netaly
> Khazanov
> Sent: Sunday, April 26, 2020 15:38
> To: Discussion list for GROMACS users
> Subject: [gmx-users] gromacs installati
: [gmx-users] gromacs installation (2020&2019)
Dear All,
I am trying to install gromacs 2020 and 2019 versions on CentOS release
6.10 (Final) linux system.
I passed throuht cmake compilation. Using command
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX
Dear All,
I am trying to install gromacs 2020 and 2019 versions on CentOS release
6.10 (Final) linux system.
I passed throuht cmake compilation. Using command
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
-DCMAKE_INSTALL_PREFIX=gromacs2020
April 23, 2020 9:08 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node
Hi,
Can you post the full log for the Intel system? I typically find the
real
cycle and time accounting section a better place to start debugging
performance issues.
A couple
Hi,
Affinity settings on the Talos II with Ubuntu 18.04 kernel 5.0 works fine.
I get threads pinned where they should be (hwloc confirmed) and consistent
results. I also get reasonable thread placement even without pinning (i.e.
the kernel scatters first until #threads <= #hwthreads). I see only
> The following lines are found in md.log for the POWER9/V100 run:
>
> Overriding thread affinity set outside gmx mdrun
> Pinning threads with an auto-selected logical core stride of 128
> NOTE: Thread affinity was not set.
>
> The full md.log is available here:
>
r the Intel run is here:
> >>
> >>
> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100
> >>
> >> Thanks for the info on constraints with 2020. I'll try some runs with
> >> different values of -pinoffset for 2019.6.
on behalf of Szilárd Páll
Sent: Friday, April 24, 2020 10:23 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node
Using a single thread per GPU as the linked log files show is not
sufficient for GROMACS (and any modern machine should have
Sent: Thursday, April 23, 2020 9:08 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node
>
> Hi,
>
> Can you post the full log for the Intel system? I typically find the real
> cycle and time accounting section a better place to
gmx-users-boun...@maillist.sys.kth.se> on behalf of Kevin
Boyd
Sent: Thursday, April 23, 2020 9:08 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node
Hi,
Can you post the full log for the Intel system? I typically find the real
cycle and tim
t NIST is having the same or similar problems with
> POWER9/V100.
>
> Jon
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Kevin
> Boyd
> Sent: Thursday, April 23, 2
or similar problems with POWER9/V100.
Jon
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Kevin Boyd
Sent: Thursday, April 23, 2020 9:08 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node
Hi
Hi,
Can you post the full log for the Intel system? I typically find the real
cycle and time accounting section a better place to start debugging
performance issues.
A couple quick notes, but need a side-by-side comparison for more useful
analysis, and these points may apply to both systems so
ustin Lemkul
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS mdp file for doing a single point
energy after acpype conversion
Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4f...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 4/23/20 5:42 AM, ABEL Stephane wrote:
We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an IBM
POWER9/V100 node versus an Intel Broadwell/P100. Both are running RHEL 7.7 and
Slurm 19.05.5. We have no concerns about GROMACS on our Intel nodes. Everything
below is about of the POWER9/V100 node.
We ran the RNASE
On 4/23/20 5:42 AM, ABEL Stephane wrote:
Deal all,
I am using acpype to convert a set of glycolipids modeled with the GLYCAM06
force fiedl into the GROMACS format. acpype works well for this task. But I
would like to check if the conversion is correctly done by performing single
point
Deal all,
I am using acpype to convert a set of glycolipids modeled with the GLYCAM06
force fiedl into the GROMACS format. acpype works well for this task. But I
would like to check if the conversion is correctly done by performing single
point energy (SPE) calculations with Amber and
To: gmx-us...@gromacs.org
Subject: [gmx-users] GROMACS PBS GPU JOB submission
Hi everyone
I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue
system is PBS. I am having some issues with the GPU selection, what I want
is to use 1 GPU per job but GROMACS is always using all
Hi everyone
I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue
system is PBS. I am having some issues with the GPU selection, what I want
is to use 1 GPU per job but GROMACS is always using all the four GPUs.
My submission script is the following:
#PBS -l
Hi,
It was not gromacs 2020, but my fault and mixing up various tools
(grompp, mdrun) from 2019 and 2020 versions.
I am sorry.
Bests,
Tamas
On 4/14/20 4:44 PM, Tamas Hegedus wrote:
Hi,
There might be some bug(?) in gromacs 2020. I can not decide.
I just installed 2020.1 today using the
Hi,
There might be some bug(?) in gromacs 2020. I can not decide.
I just installed 2020.1 today using the same script (and libraries) what
I have used for gromacs 2019.
After energy minimization, in the nvt equilibration run, it stops:
Fatal error:
Step 0: The total potential energy is
On 4/10/20 11:04 AM, Yasaman KARAMI wrote:
Dear GROMACS developers,
I am performing classical MD simulations of a membrane protein system, using
GROMACS 2018.6 version. I have just noticed that after few nano seconds, the
box dimensions are changing. Meaning that the system shrinks along
Dear GROMACS developers,
I am performing classical MD simulations of a membrane protein system, using
GROMACS 2018.6 version. I have just noticed that after few nano seconds, the
box dimensions are changing. Meaning that the system shrinks along the z-axis,
for example dimensions are changing
Hi Paul,
Thank you so much for your reply! That is very helpful.
Best,
Wei-Tse
On Mon, Apr 6, 2020 at 1:23 AM Paul bauer wrote:
> Hello,
>
> you are using a plumed modified version that adds extra options to mdrun.
> Our unit tests check that the output from mdrun -h stays invariant, and
>
Hello,
you are using a plumed modified version that adds extra options to mdrun.
Our unit tests check that the output from mdrun -h stays invariant, and
this is no longer the case once you modify the code for plumed.
You can ignore this failure in this case, but please mention in the
future
Dear gmx users,
Recently I've been trying to install GROMACS 20201. After successfully
compilng GROMACS 2020.1, when executing make check command, I
encountered the following error. Specifically, one out of 56 tests failed,
which was related to Mdrun Test.WritesHelp. Looking at the error message,
Hello gmx-users!
We have been working behind the scenes the last few months on some
changes to the organization of the GROMACS project, one of them is
switching our gmx-users mailing list to a forum
We are continuously re-thinking about how we can best engage with you
and how people can get
Hi all,
I've seen that recent tip7p water model
(https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out.
However, I couldn't find or I missed where the itp and gro files are deposited.
Anybody knows where to find them?
Thanks a lot in advance!
Best,
Jacek
Also,
please don't use Release candidate versions for anything serious.
Instead use the latest official release that suits you.
Cheers
Paul
On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote:
Hi everyone,
I'm a beginner user of GROMACS, and I'm having some troubles with the
Hello,
you can't attach files to the list here, either paste the error directly
from the terminal or upload the file somewhere and share the link.
Cheers
Paul
On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote:
Hi everyone,
I'm a beginner user of GROMACS, and I'm having some troubles
Hi everyone,
I'm a beginner user of GROMACS, and I'm having some troubles with the
installation. I follow the instruction in
http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html ,
but when i run "make", appear the error shown in file attached.
Any advice will be appreciated.
Hello gmx users!
I just finished the transition of our project database to use the Gitlab
servers.
This means that from now on issues should be reported using the issue
tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of
redmine.gromacs.org.
The redmine and gerrit servers have
Hi,
You should not send any GROMACS developer personal emails but use gmx-users
mailinglist.
You get the 404 because the comma at the end of the URL. Without it the link
should work. As context the old archived email is:
Hello,
if you have found a bug in the multi-dimensional array please report it
on redmine.gromacs.org so we can fix it, together with the build
configuration that causes it.
Cheers
Paul
On 14/03/2020 00:51, Alexander Tzanov wrote:
The new version from March 2020.1 is buggy. Try version
The new version from March 2020.1 is buggy. Try version 2020. There is another
bug in multidimensional array ...
Alex
On Mar 13, 2020 1:54 PM, xuan Zhang wrote:
Hi,
When I install the Gromacs on Linux, the cmake occurs error like below. I
am a newer on this software. I appreciate very much
For that error you may use normal and better Intel compiler or gcc above 6.3.
The 2020.1 compiles well after correcting stupid bug in multidimensional array
routine and with use of Intel 19 and gcc above 6. I use 7.3
Your compiler is too old to support C++14 but there other problem as well
Hi，
For now, I have added the compiler to cmake and it works. But in the
*make *step,
the errors were shown as below. Thank you very much.
Best regards,
Xuan
src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make:79: recipe for target
Hi,
When I install the Gromacs on Linux, the cmake occurs error like below. I
am a newer on this software. I appreciate very much that you can help me.
Best regards,
Xuan
**/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at
> The paper information is as below :
> Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic
> Light-Emitting Diode Films
> Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J.
> Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R.
>
The paper information is as below :
Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic
Light-Emitting Diode Films
Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J.
Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R.
Gentle, Alan E.
> I was planning to put the velocities in the .gro file from which I am
> inserting the molecules. If the gmx insert-molecules will ignore the
> velocities of the atoms, can you please guide me how can I insert the
> molecules with a velocity ?
> I have read a paper which mentions that they
I was planning to put the velocities in the .gro file from which I am
inserting the molecules. If the gmx insert-molecules will ignore the
velocities of the atoms, can you please guide me how can I insert the
molecules with a velocity ?
I have read a paper which mentions that they inserted the
On 3/11/20 9:56 AM, Mohamed Abdelaal wrote:
I want to insert an atom with a velocity moving downwards toward the
graphene sheet in my box.
Yes I need to remove any atom moving away from my substrate or the
deposited atoms and far by 0.4 nm.
Then repeat the process until I have inserted 3000
I want to insert an atom with a velocity moving downwards toward the
graphene sheet in my box.
Yes I need to remove any atom moving away from my substrate or the
deposited atoms and far by 0.4 nm.
Then repeat the process until I have inserted 3000 atoms.
Thanks for your reply.
Mohamed
On Wed,
Write a script that calls gmx insert-molecules 3000 times and uses the
previous output as input for each call.
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html
Is there something you have to do in between each insertion?
- John
> Hello everybody,
>
> I am
Hello everybody,
I am trying to insert molecules into a box but I have to insert one single
molecule at a time reaching 3000 molecule in total. Is there a way to
automate this process ?
Thanks
Mohamed
--
Gromacs Users mailing list
* Please search the archive at
Hi,
The code is tested extensively on a range of compilers, so we believe it is
correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS
tests with 6.4.0, so the issue might have been fixed in the meantime. As
newer versions of gcc and cuda will give better performance, I suggest
Hi all
After attempting to install GROMACS 2020 on new system, I get the error below.
The system details & other details are below the error.
cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020
-DCMAKE_C_COMPILER=gcc
Den 2020-03-07 kl. 17:04, skrev Rolly Ng:
Dear Gromacs developers,
I am new to Gromacs and I have recently compiled Gromacs 2020.
I tried to run the ADH benchmarks from
ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz
The adh_cubic and adh_dodec completed
Dear Gromacs developers,
I am new to Gromacs and I have recently compiled Gromacs 2020.
I tried to run the ADH benchmarks from
ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz
The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites
and
Dear Gromacs developers,
I am new to Gromacs and I have recently compiled Gromacs 2020.
I tried to run the ADH benchmarks from
ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz
The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites
and
Hi GROMACS users,
The official release of GROMACS 2020.1 is available!
This first patch release fixes several issues found since the initial
release of GROMACS 2020. We encourage all users of the 2020
series to update to 2020.1. Please see the link to the release notes
below for more details.
Hi GROMACS users,
The official release of GROMACS 2019.6 is available!
The sixth patch release fixes several issues found since the previous
patch release of GROMACS 2019.
We encourage all users of the 2019 series to update to 2019.6.
Please see the link to the release notes below for more
Den 2020-02-06 kl. 15:15, skrev Kneller, Daniel:
Hi Dr. van der Spoel,
I had hoped to reply using the user-lists but I realize now that I had
the user-lists in digest mode and did not want to start another thread.
CC-ing there anyway just such that it gets archived.
Thank you for responding
On 2/5/20 4:58 AM, Vedat Durmaz wrote:
Hi there,
I'm pretty sure it's not a feature but a bug which I've faced in the GMX
versions 2018.7, 2019.5 an 2020.
When I try to calculate RMSD values for a protein system including a
catalytic magnesium ion "Mg" using the command
gmx rms -s mol.pdb
Hi there,
I'm pretty sure it's not a feature but a bug which I've faced in the GMX
versions 2018.7, 2019.5 an 2020.
When I try to calculate RMSD values for a protein system including a
catalytic magnesium ion "Mg" using the command
gmx rms -s mol.pdb -f mol.xtc -f2 mol.xtc -o mol-rmsd.xvg
Dear Ryan,
On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz wrote:
> Dear Szilárd,
>
> Thank you so much for your help. I performed the following steps
> and it seems to have built successfully, I'll let you know if it does not
> run correctly as well.
>
> rm -r gromacs-2020/
> sudo
Dear Szilárd,
Thank you so much for your help. I performed the following steps
and it seems to have built successfully, I'll let you know if it does not
run correctly as well.
rm -r gromacs-2020/
sudo apt-get install gcc-8 g++-8
tar -xvzf gromacs-2020.tar.gz
cd gromacs-2020/
mkdir build
Dear Ryan,
On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz wrote:
> Dear Szilárd,
>
> Thank you for your quick response. You are correct, after
> issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
>
gcc 9 is not supported with CUDA, as far as I know version 8 is the latest
Dear Szilárd,
Thank you for your quick response. You are correct, after
issuing sudo apt-get install gcc-9 g++-9 CMake was run with:
CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON
Hi Ryan,
The issue you linked has been worked around in the build system, so my
guess is that the issue you are seeing is not related.
I would recommend that you update your software stack to the latest version
(both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should
be able to
Hello Gromacs experts,
First things first, I apologize for any double post but I just
joined the community so I'm very new and only found 1-2 posts related to my
problem but the solutions did not work. I have been doing MD for about
6-months using NAMD but want to also try out Gromacs.
Good catch Kevin, that is likely an issue -- at least part of it.
Note that you can also use the mdrun -multidir functionality to avoid
having to manually manage mdrun process placement and pinning.
Another aspect is that if you leave half of the CPU cores unused, the cores
in use can boost to a
Hi,
A few things besides any Ryzen-specific issues. First, your pinoffset for
the second one should be 16, not 17. The way yours is set up, you're
running on cores 0-15, then Gromacs will detect that your second
simulation parameters are invalid (because from cores 17-32, core 32 does
not exist)
Hello again,
I got notified that there is an issue for the first link, it needs to be
without the final dot:
http://manual.gromacs.org/2020/release-notes/index.html
Sorry for the inconvenience and happy new year!
Cheers
Paul
On 01/01/2020 18:11, Paul bauer wrote:
Hello GROMACS users!
Hello,
we only added full detection and support for the newer Rizen chip-sets
with GROMACS 2019.5, so please try if the update to this version solves
your issue.
If not, please open an issue on redmine.gromacs.org so we can track the
problem and try to solve it.
Cheers
Paul
On 02/01/2020
Hi,
happy new year!
Now to my problem:
I use Gromacs 2019.3 and to try to run some simulations (roughly 30k
atoms per system) on my PC which has the following configuration:
CPU: Ryzen 3950X (overclocked to 4.1 GHz)
GPU #1: Nvidia RTX 2080 Ti
GPU #2: Nvidia RTX 2080 Ti
RAM: 64 GB
PSU:
Hello GROMACS users!
The official release of GROMACS 2020 is now available.
What new things can you expect? Please see the release notes highlights at
http://manual.gromacs.org/2020/release-notes/index.html.
You can find the code, manual, release notes, installation instructions and
test suite
. Dezember 2019 15:54
An: gromacs.org_gmx-users@maillist.sys.kth.se; gmx-annou...@gromacs.org
Betreff: [gmx-users] GROMACS 2020 release candidate
Hi GROMACS users,
The GROMACS 2020 release candidate is now out and available!
As before, we are making the testing versions available for you to be able
Hi GROMACS users,
The official release of GROMACS 2019.5 is available!
The fifth patch release fixes several issues found since the previous
patch release of GROMACS 2019.
We encourage all users of the 2019 series to update to 2019.5.
Please see the link to the release notes below for more
; gmx-annou...@gromacs.org
Betreff: [gmx-users] GROMACS 2020 release candidate
Hi GROMACS users,
The GROMACS 2020 release candidate is now out and available!
As before, we are making the testing versions available for you to be able to
get feedback on how well things are working, and what could
Hi GROMACS users,
The GROMACS 2020 release candidate is now out and available!
As before, we are making the testing versions available for you to be
able to get feedback
on how well things are working, and what could be improved or if there
are any bugs
in the code we have missed ourselves.
Hi,
The fftw build you are trying to do uses gcc by default, and your gcc is so
old that AVX512 didn't exist yet, so it cant compile for it. Since you're
using the Intel compiler, it's easiest to also use its fft library with
cmake -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl
Harder is to
Hi everyone,
I am having some issues with the installation of Gromacs using the
optimization flag -DGMX_SIMD=AVX_512.
If I install without the optimization, everything goes ok and the software
works fine. But, as recommended by Gromacs in the log file, I should
compile using the optimization
Hi,
I suspect that you have multiple versions of hwloc on your system, and
somehow the environment is different at cmake time and make time (e.g.
different modules loaded?). If so, don't do that. Otherwise, cmake
-DGMX_HWLOC=off will work well enough. I've proposed a probably fix for
future 2019
Hello,
I'm trying to install gromacs-2019.4 with GPU support, but was always wrong.
I ran cmake as
cmake3 .. -DCMAKE_INSTALL_PREFIX=~/gromacs/gmx2019.4 -DGMX_BUILD_OWN_FFTW=ON
-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_HWLOC=ON
It works but when installing always get error
Dear Gromacs Developers,
I'm trying to install the 2018.8 version of GROMACS through the Spack
package manager (https://spack.io). They have packaged GROMACS, but I
have noticed a SHA256 checksum mismatch. They have
'3776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebec' on
file, while
I managed to follow the tutorial on replica exchange by Mark Abraham. It?s
really great tutorial and GROMACS works amazingly fast.
Can someone point me please to the research paper(s) that describe some
real life experiments or benchmarks running replica exchange simulations
with GROMACS?
I
Can you please file an issue on redmine.gromacs.org and attach the inputs
that reproduce the behavior described?
--
Szilárd
On Wed, Dec 4, 2019, 21:35 Chenou Zhang wrote:
> We did test that.
> Our cluster has total 11 GPU nodes and I ran 20 tests over all of them. 7
> out of the 20 tests did
We did test that.
Our cluster has total 11 GPU nodes and I ran 20 tests over all of them. 7
out of the 20 tests did have the potential energy jump issue and they were
running on 5 different nodes.
So I tend to believe this issue happens on any of those nodes.
On Wed, Dec 4, 2019 at 1:14 PM
The fact that you are observing errors alo the energies to be off by so
much and that it reproduces with multiple inputs suggest that this may not
a code issue. Did you do all runs that failed on the same hardware? Have
you excluded the option that one of those GeForce cards may be flaky?
--
We tried the same gmx settings in 2019.4 with different protein systems.
And we got the same weird potential energy jump within 1000 steps.
```
Step Time
00.0
Energies (kJ/mol)
BondU-BProper Dih. Improper Dih. CMAP Dih.
Hi,
I've run 30 tests with the -notunepme option. I got the following error
from one of them(which is still the same *cudaStreamSynchronize failed*
error):
```
DD step 1422999 vol min/aver 0.639 load imb.: force 1.1% pme
mesh/force 1.079
Step Time
1423000
For the error:
```
^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9
M-cycles
^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4
M-cycles
/var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation
fault gmx mdrun -v -s $TPR -deffnm
Hi,
What driver version is reported in the respective log files? Does the error
persist if mdrun -notunepme is used?
Mark
On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, wrote:
> Hi Gromacs developers,
>
> I'm currently running gromacs 2019.4 on our university's HPC cluster. To
> fully utilize the
Hi Gromacs developers,
I'm currently running gromacs 2019.4 on our university's HPC cluster. To
fully utilize the GPU nodes, I followed notes on
http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html.
And here is the command I used for my runs.
```
gmx mdrun -v -s
gt;>>>>>>
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: Monday, November 25, 2019 11:03:03 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Gromacs - Difference between target temperature and
pressure in mdp and
On 11/25/19 2:15 PM, Fabio Bologna wrote:
Dear Gromacs user-base and experts,
I need your help, as a Gromacs rookie. I've been trying to simulate the
folding of a 20 residues mini-protein inside a dodecahedric explicit solvent
box (30542 atoms) using Gromacs 2016.1. Because I need to
Re pressure, did you check the graph of what the pressure is doing?
The variation between steps of the pressure can be huge, hundreds of bar
when the average is meant to be 1. So it is not surprising that the average
isn't exactly 1. See below link for a couple of examples. Note as the
system
Dear Gromacs user-base and experts,
I need your help, as a Gromacs rookie. I've been trying to simulate the
folding of a 20 residues mini-protein inside a dodecahedric explicit solvent
box (30542 atoms) using Gromacs 2016.1. Because I need to start from the linear
structure, my box is
Hi Gromacs team,
We are installing Gromacs in our environment, with five servers Linux
Centos 6. We need use the Gromacs in cluster, because we need
make jobs more fast. But we notice that the use of the processor machine is
in just one of the servers, in the same server that we started the
Hi,
Please direct GROMACS usage questions to the users' list. Replying there,
make sure you are subscribed and continue the conversation there.
The issue is that you requested static library detection, but the hwloc
library dependencies are not correctly added to the GROMACS link
dependencies.
On 10/11/19 9:44 AM, Suprim Tha wrote:
Sorry to disturb you again. It would be of immense help if you could please
help me with this one.
During energy minimization with gmx mdrun -v -deffnm em ; I did not get any
results. The earlier code run was
What do you mean "did not get any results?"
Sorry to disturb you again. It would be of immense help if you could please
help me with this one.
During energy minimization with gmx mdrun -v -deffnm em ; I did not get any
results. The earlier code run was
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
and I used em.mdp file
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