[gmx-users] Ethanol Co-ordinate file

Samuel Flores samuelfloresc at gmail.com
Thu Aug 4 00:01:51 CEST 2016


I have been plagued with an odd backup issue that I don't understand. Gromacs seems to be making scads of successive backups of certain files, even in a single run. This often leads to death due to an excess of backups. Here is the first error:

Program gmx grompp, VERSION 5.1.2
Source code file: /local/easybuild/build/GROMACS/5.1.2/intel-2016a-hybrid/gromacs-5.1.2/src/gromacs/utility/futil.cpp, line: 409

Fatal error:
Won't make more than 99 backups of ions.tpr for you.
The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Halting parallel program gmx grompp on rank 67 out of 120
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 67
Calculating fourier grid dimensions for X Y Z

.. which I believe is due to this command:

   gmx_mpi grompp -f ions.mdp -c threaded-truncated_solv.gro -p topol.top -o ions.tpr

For now I set export GMX_MAXBACKUP=-1. But it would be nice to know what is actually happening. Can anyone help? I append my SLURM job file below.

I would also like it if someone told me what is up with these ranks .. Not having worked much with MPI, I have the vague impression that these are processes or threads. In any case why are these processes being killed? Is this normal?

Many thanks,


[samuelf at aurora1 proteinA-mine]$ cat job.proteinA-mine 
#!/bin/bash -l
#SBATCH -J mine   
#SBATCH --tasks-per-node=20 
#SBATCH --exclusive 
#SBATCH -A snic2015-16-49
#SBATCH -t 168:00:00
# tried -N12. timed out. trying 6 now.

# Disable backups. These have been causing problems for unclear reasons

# End part that is written in /home/samuelf/svn/breeder/src/Breed.cpp:87

# From here down, This file is generated in /home/samuelf/svn/breeder/src/MysqlConnection.cpp:97
cd /lunarc/nobackup/users/samuelf/proteinA-mine/
echo " now working in : /lunarc/nobackup/users/samuelf/proteinA-mine/" 
cp /home/samuelf/svn/breeder//singleMutantFiles/ions.mdp /lunarc/nobackup/users/samuelf/proteinA-mine/ ; 
cp /home/samuelf/svn/breeder//singleMutantFiles/md.mdp /lunarc/nobackup/users/samuelf/proteinA-mine/ ; 
#cp /home/samuelf/svn/breeder//singleMutantFiles/mdout.mdp /lunarc/nobackup/users/samuelf/proteinA-mine/ ; 
cp /home/samuelf/svn/breeder//singleMutantFiles/minim.mdp /lunarc/nobackup/users/samuelf/proteinA-mine/ ; 
cp /home/samuelf/svn/breeder//singleMutantFiles/npt.mdp /lunarc/nobackup/users/samuelf/proteinA-mine/ ; 
cp /home/samuelf/svn/breeder//singleMutantFiles/nvt.mdp /lunarc/nobackup/users/samuelf/proteinA-mine/ ; 
# Write cluster-specific configuration and module load commands.. 
# The following portion is being read from >/home/samuelf/svn/breeder//singleMutantFiles/gromacs-commands.txt< 

# Comment in original file: /home/samuelf/projects/1FC2.domainZ/gromacs-commands.txt
#module load intel/2016a
module load       icc/2016.1.150-GCC-4.9.3-2.25  impi/
module load GROMACS/5.1.2-hybrid

# End portion from >/home/samuelf/svn/breeder//singleMutantFiles/gromacs-commands.txt< 
echo 6 > temp.txt
echo 1 >> temp.txt
echo " Check 1"
cat temp.txt | srun -n 1 gmx_mpi pdb2gmx -f threaded-truncated.pdb -o threaded-truncated_processed.gro -ignh
echo " Check 2"
#6: Amber sb99 , 3 point TIP3P water model: force field was selected based on this benchmark article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/
srun  gmx_mpi editconf -f threaded-truncated_processed.gro -o threaded-truncated_newbox.gro -c -d 1.0 -bt cubic
echo " Check 3"
srun  -n 1 gmx_mpi solvate -cp threaded-truncated_newbox.gro -cs spc216.gro -o threaded-truncated_solv.gro -p topol.top
# threaded-truncated_solv.gro has full length SpA:
echo " Check 4"
srun  gmx_mpi grompp -f ions.mdp -c threaded-truncated_solv.gro -p topol.top -o ions.tpr
# threaded-truncated_solv_ions.gro has the full length SpA:
echo " Check 5"
echo 13 | srun -n 1 gmx_mpi genion -s ions.tpr -o threaded-truncated_solv_ions.gro -p topol.top -pname NA -neutral 
# previously had erroneous srun  -n 1gmx_mpi ... :
echo " Check 6"
srun  -n 1 gmx_mpi grompp -f minim.mdp -c threaded-truncated_solv_ions.gro -p topol.top -o em.tpr
echo " Check 7"
srun  gmx_mpi mdrun -v -deffnm em
# em.gro has only one domain for some reason
echo " Check 8"
srun  -n 1 gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
echo " Check 9"
srun  gmx_mpi mdrun -deffnm nvt
echo " Check 10"
srun  -n 1 gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
echo " Check 11"
srun  gmx_mpi mdrun -deffnm npt
echo " Check 12"
srun  -n 1 gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
echo " Check 13"
srun  gmx_mpi mdrun -deffnm md_0_1
# insert DSSP commands here
# End of GROMACS command generator./home/samuelf/svn/breeder/src/MysqlConnection.cpp:161
# Returning from /home/samuelf/svn/breeder/src/MysqlConnection.cpp:163

Samuel Coulbourn Flores 
Computational and Systems Biology Program
Department of Cell and Molecular Biology
Uppsala University

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