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#37417 - 03/21/19 08:14 AM Re: Free version of CHARMM in parallel [Re: pmj]
SNOW001 Offline
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Registered: 11/12/18
Posts: 16
./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

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#37420 - 03/21/19 08:49 AM Re: Free version of CHARMM in parallel [Re: pmj]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
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

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#37424 - 03/21/19 09:48 AM Re: Free version of CHARMM in parallel [Re: pmj]
tru Offline
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Registered: 01/30/04
Posts: 8
Loc: France
$ /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

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#37430 - 03/22/19 04:24 AM Re: Free version of CHARMM in parallel [Re: pmj]
pmj Offline
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Registered: 01/15/19
Posts: 46
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.



Edited by pmj (03/22/19 07:00 AM)

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#37431 - 03/25/19 04:48 AM Re: Free version of CHARMM in parallel [Re: pmj]
SNOW001 Offline
Forum Member

Registered: 11/12/18
Posts: 16
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.

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#37432 - 03/25/19 05:55 AM Re: Free version of CHARMM in parallel [Re: SNOW001]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
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!


Edited by pmj (03/25/19 07:00 AM)

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#37433 - 03/25/19 07:58 AM Re: Free version of CHARMM in parallel [Re: pmj]
SNOW001 Offline
Forum Member

Registered: 11/12/18
Posts: 16
Have you try only using gbsw, or only using eef1, I think they can parallel.


Edited by SNOW001 (03/25/19 08:00 AM)

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#37434 - 03/25/19 08:09 AM Re: Free version of CHARMM in parallel [Re: SNOW001]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
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.

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#37435 - 03/25/19 08:23 AM Re: Free version of CHARMM in parallel [Re: pmj]
SNOW001 Offline
Forum Member

Registered: 11/12/18
Posts: 16
Could you paste your input file, may be I can test it with my computer.


Edited by SNOW001 (03/25/19 08:24 AM)

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#37436 - 03/26/19 05:42 AM Re: Free version of CHARMM in parallel [Re: SNOW001]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
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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