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#37268 - 01/11/19 07:53 PM Charmm in Ubuntu can not perform parallel computing
tyrion_jj Offline
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Registered: 01/08/19
Posts: 19
Hello everyone,

My server is Ubuntu. When I perform the command line "nohup mpirun -np 32 charmm setup1.out & ", only one CUP core can calculate. Ubuntu needs what libraries to run the charmm?
Can anyone help me? Thanks advance!

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#37269 - 01/11/19 08:09 PM Re: Charmm in Ubuntu can not perform parallel computing [Re: tyrion_jj]
tyrion_jj Offline
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Registered: 01/08/19
Posts: 19
I have installed below libraries:
"apt install w3m w3m-img openmpi-bin libopenmpi-dev gcc g++ gfortran tcl grace \
samba cifs-utils samba-common cp2k bc csh flex xorg-dev zlib1g-dev libbz2-dev patch \
gromacs mpich bc csh flex xorg-dev zlib1g-dev libbz2-dev patch cmake"

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#37270 - 01/11/19 09:30 PM Re: Charmm in Ubuntu can not perform parallel computing [Re: tyrion_jj]
rmv Online   content

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Registered: 09/17/03
Posts: 8336
Loc: 39 03 48 N, 77 06 54 W
What commands were used to build the charmm program? Were there any informational or warning messages regarding MPI from the build process?

The MPI libraries from Linux distributions typically lack the Fortran90 bindings (mpi.mod). With the GCC suite (gcc, gfortran, etc.), it is recommended to build the MPI library with Fortran90 support included, using the same compiler versions that will be used to compile charmm.

Please note that there is a specific forum for installation questions.
_________________________
Rick Venable
computational chemist


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#37271 - 01/11/19 10:07 PM Re: Charmm in Ubuntu can not perform parallel computing [Re: rmv]
tyrion_jj Offline
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Registered: 01/08/19
Posts: 19
At line 164 of file /home/hj/program/charmm/source/util/parse.src (unit = 5, file = 'stdin')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE

How can I add the Fortran90 bindings (mpi.mod)? Thanks a lot!!!

Sorry, I would put my question on the correct model next time, thank you for your replying.

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#37272 - 01/11/19 10:35 PM Re: Charmm in Ubuntu can not perform parallel computing [Re: rmv]
tyrion_jj Offline
Forum Member

Registered: 01/08/19
Posts: 19
Thank you so much !! I have solve my problem, I installed all of the libraries among c35b2.cgenff.charmm/doc/parallel.doc. And I change my command line "nohup mpirun -np 32 charmm -i 1.chm -o 1.out &" instead of the wrong previous expression "nohup mpirun -np -32 <1.chm> 1.out &" And then, the parallel computing is performed. Thanks a lot ! grin

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#37274 - 01/12/19 10:48 AM Re: Charmm in Ubuntu can not perform parallel computing [Re: tyrion_jj]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8336
Loc: 39 03 48 N, 77 06 54 W
Note that c35b2 is fairly old code, and a free version of c43b1 is available.
_________________________
Rick Venable
computational chemist


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