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Re: Free version of CHARMM in parallel
pmj #37417 03/21/19 12:14 PM
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./install.com gnu M is ok, I have not try ./install.com gnu M MPICH AMD64. What compiler do you use ?
When do ./test.com gnu_M , you may see something like this: ~/charmm/exec/gnu_M/charmm -input ~/char mm/test/c31test/gbsw.inp -prevclcg >& output/gbsw.out, it use one core, if you want 8 cores can try: mpirun -np 8 ~/charmm/exec/gnu_M/charmm -input ~/charmm/test/c31test/gbsw.inp -prevclcg >& output/c 31test/gbsw.out

Re: Free version of CHARMM in parallel
pmj #37420 03/21/19 12:49 PM
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In CHARMM give the command pref. It lists the keywords used when CHARMM was installed. If you see MPI PARALLEL in the list you have a parallel version.

Try test.com without arguments. It will tell you how to run the testcases in parallel.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Free version of CHARMM in parallel
pmj #37424 03/21/19 01:48 PM
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$ /bin/echo -e '*\nshow\nstop'|/c7/shared/c43b2/gcc-openmpi-2.1.5-cuda-9.2.148_396.37/bin/charmm|grep -e 'PARA' -e 'MPI'
MISCOM: label: MPI value: 1
MISCOM: label: PARAFULL value: 1
MISCOM: label: PARALLEL value: 1

Re: Free version of CHARMM in parallel
pmj #37430 03/22/19 08:24 AM
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Dear all,

I made all the tests as you have suggested and it seems CHARMM has complied properly.

From the data I obtained, it seems that GBSW and EMAP, however, are not really parallelised. Is it possible to actually parallelised GBSW and EMAP by switching on some options in the code?

I was wondering if EEF1 is parallelised perhaps and if it is possible to use emap constraints with it?

Thank you all for help.


Last edited by pmj; 03/22/19 11:00 AM.
Re: Free version of CHARMM in parallel
pmj #37431 03/25/19 08:48 AM
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Both GBSW and EEF1 can parallel, I am not sure about EMAP. When view file charmm/source/emap/emapdock.src emapfield.src emapop.src emapsubs.src, only emapsubs.src has key words:
#if KEY_PARALLEL==1
use parallel
I am not sure which command to call when you run (may be it will display in run.out if you add 'PRNLEV 15' in your run.inp file, or may not).
If emapdock.src, emapfield.src or emapop.src were used, I guess it cannot parallel. Actually, I'm not familiar with EMAP.

Re: Free version of CHARMM in parallel
SNOW001 #37432 03/25/19 09:55 AM
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Hi!

First of all thanks for your help.

I checked the files for emap and as you said and in the emapsubs.src:

#if KEY_PARALLEL==1
NSTA=(NEMAT*MYNOD)/NUMNOD+1
NEND+(NEMAT*MYNODP)/NUMNOD
#else /**/
NSTA=1
NEND=NEMAT

The thing is when I test the same scripts with gbsw or eef1 and emap (in all combinations w or w/o gbsw or eef1 and emap) and I measure the time I get random values (the time does not decrease when I use more cores.

My system is quite large (120 000 atoms) so it is really important for me to have gbsw or eef1 and emap parallelised properly. Initially, I thought I complied charmm wrongly, but I checked some scripts with explicit solvent and they are rather fast with 16 cores (with 4 cores it is approx 10 min and with 16 is around 4-5 min). I do not get the same with gbsw, eef1 or when I use emap.

Also, I was wondering is it possible to comple free version charmm with

./install gnu xxlarge ifort x86_64 i8 D M MPICH?

Thank you!

Last edited by pmj; 03/25/19 11:00 AM.
Re: Free version of CHARMM in parallel
pmj #37433 03/25/19 11:58 AM
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Have you try only using gbsw, or only using eef1, I think they can parallel.

Last edited by SNOW001; 03/25/19 12:00 PM.
Re: Free version of CHARMM in parallel
SNOW001 #37434 03/25/19 12:09 PM
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I tested it and for gbsw I get normal reduction in cpu time when I remove mandatory nonbonded keywords.

For eef1 it seems it not parallelised if I use emap.

Re: Free version of CHARMM in parallel
pmj #37435 03/25/19 12:23 PM
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Could you paste your input file, may be I can test it with my computer.

Last edited by SNOW001; 03/25/19 12:24 PM.
Re: Free version of CHARMM in parallel
SNOW001 #37436 03/26/19 09:42 AM
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Hi!

Thank you for testing it.

Since I could not send the files through forum here I uploaded it to:

https://ufile.io/pmsao

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