Dear All,
I have upgraded my Gromacs v4.5.5 to 5.0. I am unable to run parallel minimization and simulation in cluster. Previously (v4.5.5) I was simulating using the command “mdrun –v –s em.tpr –nt 30 &” but, this command is not working in v5.0 (also tried using -ntmpi 20) and giving the below mentioned errors. The command as per the Dr. Justin tutorial “gmx mdrun -v -deffnm em” is also not working for my cluster installation, but running fine in my local computer (both having gromacs v5.0). Kindly help me how to run minimization using mdrun in parallel.
The installation I followed for CGI cluster is as follows
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cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX:PATH=/user1/tanpaku/bussei/bics@1986/Bikash/cmake/gro/gro5.0 -DGMX_MPI=ON -DGMX_BUILD_SHARED_LIBS=ON
make
make install
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ERROR
GROMACS: gmx mdrun, VERSION 5.0
Executable: Bikash/cmake/gro/gro5.0/bin/gmx
Library dir: Bikash/cmake/gro/gro5.0/share/gromacs/top
Command line:
gmx mdrun -nt 30 -deffnm em
Back Off! I just backed up em.log to ./#em.log.1#
Number of hardware threads detected (288) does not match the number reported by OpenMP (276).
Consider setting the launch configuration manually!
Reading file em.tpr, VERSION 5.0 (single precision)
The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 6
Non-default thread affinity set, disabling internal thread affinity
Using 5 MPI threads
Segmentation fault
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Thanking you
In anticipation of your reply
Bikash
Osaka, Japan
Dear RG members,
I have fixed this problem in my cluster. Thank you very much for your suggestions. In addition, I would like to inform about the OMP_NUM_THREADS mismatching. If anyone is getting such errors, kindly add unsetenv OMP_NUM_THREADS in your environment or type in your terminal. SGI Altix UV users may face such kind of errors in gcc.
Best regards
Bikash
I would like to remind you that calculation time strongly depends on number of CPU. Sometimes, using more number of CPU also slows down calculation time. It is useful to test running 10 ps simulation using various number of CPU . At the and of the .log file will be shown simulation time then you will find optimal number of CPU in order to run simulation saving you time.
Dear RG members,
I have fixed this problem in my cluster. Thank you very much for your suggestions. In addition, I would like to inform about the OMP_NUM_THREADS mismatching. If anyone is getting such errors, kindly add unsetenv OMP_NUM_THREADS in your environment or type in your terminal. SGI Altix UV users may face such kind of errors in gcc.
Best regards
Bikash
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