Dear all,
I already installed gromacs-5.1.2 succesfully with the following
instruction :
tar xfz gromacs-5.1.2.tar.gz
cd gromacs-5.1.2
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
However, after finishing
ption to
> use it the old way as well.
>
> Regards,
> James
>
>
> On 05/04/16 08:19, Husen R wrote:
>
>> Dear all,
>>
>> I already installed gromacs-5.1.2 succesfully with the following
>> instruction :
>>
>> tar xfz gromacs-5.1.2.tar.gz
Hi all,
Currently, I'm trying to run mdrun command in parallel.
the following is my batch script using Slurm as a resource manager:
=Batch Script==
#!/bin/bash
#SBATCH -J Eq1
#SBATCH -o eq1-%j.out
#SBATCH -A pro
#SBATCH -N 2
#SBATCH -n 16
gmx mdrun -deffnm tpr
Hi all,
I tried to run mdrun on more than one node using the command available in
this url
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html
.
The following is my sbatch job :
###SBATCH
#!/bin/bash
#SBATCH -J sim
#SBATCH -o md-
robably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R wrote:
>
> > Hi all,
> >
> &g
;
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R wrote:
>
> > Hi all,
> >
> &g
Hi,
>
> Probably you haven't built gromacs with MPI support, else the name of the
> binary would be gmx_mpi. You can get that confirmed if you look further
> down the output .log files.
>
> Mark
>
> On Wed, 20 Apr 2016 10:09 Husen R wrote:
>
> > Hi all,
&g
g the lines of
>
> mpirun -np 2 gmx_mpi mdrun
>
> or
>
> mpirun -np 2 mdrun_mpi
>
> if the admins have done an mdrun-only installation.
>
> I'll fix that for future versions
>
> Mark
>
> On Wed, 20 Apr 2016 13:34 Husen R wrote:
>
> >
Dear all,
is there any complete documentation discussing checkpoint/restart in
Gromacs-5.1.2 ?
I found this link that discuss checkpoint (
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
this link that discuss restart (
http://www.gromacs.org/Documentation/How-tos/Doing_Res
Hi,
Thanks a lot !
I'll try it,..
Regards,
Husen
On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul wrote:
>
>
> On 4/24/16 12:04 AM, Husen R wrote:
>
>> Dear all,
>>
>> is there any complete documentation discussing checkpoint/restart in
>> Gromacs-
BATCH --mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
Thank you in advance
Regards,
Husen
On Sun, Apr 24, 2016 at 7:57 PM, Husen R wrote:
> Hi,
>
> Thanks a lot !
> I'll try it,..
>
>
: md_0_1.cpt and
md_0_1_prev.cpt
is this because of -deffnm option ?
I just want to make sure.
Regards,
Husen
On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham
wrote:
> Hi,
>
> On Tue, 26 Apr 2016 06:19 Husen R wrote:
>
> > Hi all,
> >
> > I tried to run this gro
Dear all
Does simulation able to be restarted from checkpoint file with fewer nodes ?
let's say, at the first time, I run simulation with 3 nodes. At running
time, one of those nodes is crashed and the simulation is terminated.
I want to restart that simulation immadiately based on checkpoint fil
I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager.
On Sat, May 14, 2016 at 7:53 AM, Husen R wrote:
> Dear all
>
> Does simulation able to be restarted from checkpoint file with fewer nodes
> ?
> let's say, at the first time, I run simulation with 3 nodes. At ru
ustin Lemkul wrote:
>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At running
>> time, one
14, 2016 at 7:58 AM, Justin Lemkul wrote:
>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At r
aspects
> >> > (These thoughts are common to earlier versions also.)
> >> >
> >> > Mark
> >> >
> >> >
> >> > Best wishes
> >> >> James
> >> >>
> >> >> > I have found that only some kin
Hi all,
I got the following error message when I tried to restart gromacs
simulation from checkpoint file.
I restart the simulation using fewer nodes and processes, and also I
exclude one node using '--exclude=' option (in slurm) for experimental
purpose.
I'm sure fewer nodes and processes are no
PROCESSES
= PID 6983 RUNNING AT head-node
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===
On Thu, Jun 16, 2016 at 11:48 AM, Husen R wrote:
> Hi all,
>
&
e
> upon md_test.xtc, so perhaps you need to consider whether the file exists,
> is writable, etc.
>
> Mark
>
> On Thu, Jun 16, 2016 at 6:48 AM Husen R wrote:
>
> > Hi all,
> >
> > I got the following error message when I tried to restart gromacs
> > si
On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham
wrote:
> Hi,
>
> On Thu, Jun 16, 2016 at 9:30 AM Husen R wrote:
>
> > Hi,
> >
> > Thank you for your reply !
> >
> > md_test.xtc is exist and writable.
> >
>
> OK, but it needs to be seen that
kes place when the checkpoint is read is not relevant to the
> problem.
>
> Mark
>
> On Thu, Jun 16, 2016 at 9:46 AM Husen R wrote:
>
> > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham
> > wrote:
> >
> > > Hi,
> > >
> > >
Hi all,
For academic purpose, I'm wondering how does checkpoint feature in Gromacs
works ?
is there any resource/tutorial that I can learn ?
Thank you in advance,
Husen
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choosing to checkpoint at the same time.
> Pick a portable file format.
>
> Mark
>
> On Thu, Jun 23, 2016 at 4:15 AM Husen R wrote:
>
> > Hi all,
> >
> > For academic purpose, I'm wondering how does checkpoint feature in
> Gromacs
> > works
g/Documentation/Errors
On Thu, Jun 16, 2016 at 6:23 PM, Mark Abraham
wrote:
> Hi,
>
> On Thu, Jun 16, 2016 at 12:24 PM Husen R wrote:
>
> > On Thu, Jun 16, 2016 at
wrote:
> Hi,
>
> The only explanation is that that file is not in fact properly accessible
> if rank 0 is placed other than on "compute-node," which means your
> organization of file system / slurm / etc. aren't good enough for what
> you're doing.
>
>
Hi Mark,
Thank you very much!
Regards,
Husen
On Thu, Jun 23, 2016 at 3:42 PM, Mark Abraham
wrote:
> Yes
>
> On Thu, Jun 23, 2016 at 9:54 AM Husen R wrote:
>
> > Hi,
> >
> > Could you tell me the location of the code ?
> > is this the location of the c
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