[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Antara mazumdar 
Dear Mark,

Thanks for the suggestion. I will tell them that.
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Mark Abraham 
Hi,

Oh, and get them to install it properly. You should not be running from
.../build/bin

Mark

On Thu, May 26, 2016 at 10:54 AM Antara mazumdar 
wrote:

> Dear Mark,
>
>I will ask our HPC support team to check the MPI enabled version of
> gromacs then. Thank you for your suggestion.
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Antara mazumdar 
Dear Mark,

   I will ask our HPC support team to check the MPI enabled version of
gromacs then. Thank you for your suggestion.
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Mark Abraham 
Hi,

You need to build an MPI-enabled version of GROMACS, which will default to
being named gmx_mpi. Thus

/home/lipi/openmpi164/bin/mpirun -np 16
/app/setups/gromacs-5.1.1/build/bin/gmx_mpi mdrun -deffnm
step6.2_equilibration -rdd 1.8

Your run is starting 16 serial mdrun, which are then fighting over the same
checkpoint file.

Mark

On Thu, May 26, 2016 at 9:32 AM Antara mazumdar 
wrote:

> Dear Users,
>   I was trying to do equilibration of a mixed lipid vesicle using gromacs
> 5.1 in parallel using the below pasted pbs script :
>
>
> #!/bin/tcsh
> #PBS -l walltime=48:00:00
> #PBS -N VES_new_16
> #PBS -q workq
> #PBS -l select=1:ncpus=16:mpiprocs=16
> #PBS -V
>
> # Go to the directory from which you submitted the job
> cd $PBS_O_WORKDIR
>
> #export MPI_DEBUG=all
> #export MPI_IB_RAILS=2
> #export MPI_DSM_DISTRIBUTE=1
> #export MPI_VERBOSE=1
> #export MPI_BUFS_THRESHOLD=1
> #export MPI_BUFS_PER_PROC=1024
> #export OMP_NUM_THREADS=1
> #export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib
> module load intel-cluster-studio-2013
>
>
> setenv OMP_NUM_THREADS 1
> /home/lipi/openmpi164/bin/mpirun -np 16
> /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
> step6.2_equilibration -rdd 1.8 > test.dat
>
> This is generating multiple output and checkpoint files while its trying to
> run :
>
>
>  #step6.2_equilibration.xtc.6#
>  #step6.2_equilibration_step4400.cpt.1#
>  #step6.2_equilibration.log.3#
> #step6.2_equilibration.log.5#
>  #step6.2_equilibration.log.4#
>  #step6.2_equilibration.log.2#
>  step6.2_equilibration_prev.cpt
>  #step6.2_equilibration.log.6#
> step6.2_equilibration.cpt
> #step6.2_equilibration.xtc.3#
>  #step6.2_equilibration.xtc.5#
> #step6.2_equilibration.xtc.7#
> step6.2_equilibration.xtc
>
> When i check the log file to see the errors , it is showing the following :
>
>   Step   Time Lambda
>   00.00.0
>
>Energies (kJ/mol)
>Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
> 1.18159e+053.78079e+04   -8.79894e+06   -1.10782e+064.70754e+05
> Flat-bottom posres  PotentialKinetic En.   Total Energy
> Temperature
> 4.65013e+06   -4.62990e+062.25820e+02   -4.62968e+066.73923e-02
>  Pressure (bar)
>-7.74545e+01
>
> DD  step 39 load imb.: force 22.2%
>
> Writing checkpoint, step 560 at Thu May 26 11:57:56 2016
>
>
>
> ---
> Program gmx mdrun, VERSION 5.1.1
> Source code file:
> /app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670
>
> File input/output error:
> Cannot rename checkpoint file; maybe you are out of disk space?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> I am not able to find the solution for it. What could be causing this? I
> have not been able to find help from HPC support available to us.
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Antara mazumdar 
Dear Users,
  I was trying to do equilibration of a mixed lipid vesicle using gromacs
5.1 in parallel using the below pasted pbs script :


#!/bin/tcsh
#PBS -l walltime=48:00:00
#PBS -N VES_new_16
#PBS -q workq
#PBS -l select=1:ncpus=16:mpiprocs=16
#PBS -V

# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR

#export MPI_DEBUG=all
#export MPI_IB_RAILS=2
#export MPI_DSM_DISTRIBUTE=1
#export MPI_VERBOSE=1
#export MPI_BUFS_THRESHOLD=1
#export MPI_BUFS_PER_PROC=1024
#export OMP_NUM_THREADS=1
#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib
module load intel-cluster-studio-2013


setenv OMP_NUM_THREADS 1
/home/lipi/openmpi164/bin/mpirun -np 16
/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
step6.2_equilibration -rdd 1.8 > test.dat

This is generating multiple output and checkpoint files while its trying to
run :


 #step6.2_equilibration.xtc.6#
 #step6.2_equilibration_step4400.cpt.1#
 #step6.2_equilibration.log.3#
#step6.2_equilibration.log.5#
 #step6.2_equilibration.log.4#
 #step6.2_equilibration.log.2#
 step6.2_equilibration_prev.cpt
 #step6.2_equilibration.log.6#
step6.2_equilibration.cpt
#step6.2_equilibration.xtc.3#
 #step6.2_equilibration.xtc.5#
#step6.2_equilibration.xtc.7#
step6.2_equilibration.xtc

When i check the log file to see the errors , it is showing the following :

  Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.18159e+053.78079e+04   -8.79894e+06   -1.10782e+064.70754e+05
Flat-bottom posres  PotentialKinetic En.   Total Energy
Temperature
4.65013e+06   -4.62990e+062.25820e+02   -4.62968e+066.73923e-02
 Pressure (bar)
   -7.74545e+01

DD  step 39 load imb.: force 22.2%

Writing checkpoint, step 560 at Thu May 26 11:57:56 2016



---
Program gmx mdrun, VERSION 5.1.1
Source code file:
/app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670

File input/output error:
Cannot rename checkpoint file; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



I am not able to find the solution for it. What could be causing this? I
have not been able to find help from HPC support available to us.



Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.