REMC hippo_input

Discussions on how to set up simulations, typically starting from a pdb file.
sitiazma
Posts: 11
Joined: Tue Sep 15, 2009 12:29 pm

REMC hippo_input

Post by sitiazma » Mon Sep 21, 2009 1:37 pm

I am also having the same output as m.kalavera.

Regarding the hippo_input.txt temperature (T), do we need to have the same temperature as in remc_temperature.dat? or which temperature should I put?

Thank you.

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: REMC hippo_input

Post by martin » Mon Sep 21, 2009 2:07 pm

Hi,

the temperature from the input file is ignored for REMC. You need to install mpich2 and the daemon needs to be running.

Copy all hippo files into directories that have the names of the temperatures. Then use the attached config file to run REMC by executing:

>mpiexec -configfile configfile.dat

Please let me know if this runs. I also have scripts for queuing systems if you need.

Best wishes,
Martin

NB If it crashes it might be a new-line issue in linux (add an extra line at the end of the temperature file)
Attachments
configfile.dat
mpich2 configfile
(874 Bytes) Downloaded 344 times
remc_temperature.dat
temperature file
(44 Bytes) Downloaded 319 times

sitiazma
Posts: 11
Joined: Tue Sep 15, 2009 12:29 pm

Re: REMC hippo_input

Post by sitiazma » Tue Sep 22, 2009 2:22 pm

Hi

I just found out that my cluster does not having the MPICH2 installed. Is there any other way to run the REMC? However, I will try to install the MPICH2.

Regards

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: REMC hippo_input

Post by martin » Tue Sep 22, 2009 2:49 pm

Hi,

Unfortunately there is no other way. But for most systems you can just run a single MC simulation at slightly elevated temperatures, this usually gives good sampling.
Best wishes,
Martin

sitiazma
Posts: 11
Joined: Tue Sep 15, 2009 12:29 pm

Re: REMC hippo_input

Post by sitiazma » Wed Sep 23, 2009 5:05 pm

Hi Martin

I managed to install the mpich2 in my home cluster. As before, when I run the ./hippo_p3_mpi the log.txt seemed normal but the simulation actually not running at all. Then I tried to follow your suggestion as above:

what I did
1. I edit your remc_temperature.dat and configfile.dat to have only 4 temperatures to test in a node which is having 4cpus.
2. mkdir 4 directories based on the temperatures as from your configfile.dat path
/home/peptide/300
/home/peptide/336
/home/peptide/356
/home/peptide/472

3. I copied all input files into the directories: hippo_p3_mpi, hippo_input.txt, hippo_protein_database.dat, oplsaa_forcefield.dat, remc_temperature.dat, mypeptide.pdb

4. After the mpd running, I run the command mpiexec -configfile configfile.dat
I got error outputs. I have tried to change various of command and play around with the setup of the mpiexec, but still failed. I do not know whether these errors come from the way I setup the hippo remc simulation or from the mpich2

my questions are
- do I need to change the name ./hippo to ./hippo_p3_mpi in the configfile.dat?
- where actually the configfile.dat should be? or it should also in each directories?

I am sorry if the problems are due to my beginner knowledge working with mpich2 environment.

Thanks again for any helps.

Best regards,
siti

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: REMC hippo_input

Post by martin » Wed Sep 23, 2009 7:10 pm

Hi,

Yes, you need to change the name of the executable in the configure file to hippo_mpi_p3 if you are using that executable. You might have to put ./hippo_mpi_p3 for linux. The configure file just tells mpi where each replica is. Also, you might have to delete the .dat for configure.dat as i can't remember if mpich2 takes endings for the configure file (my fault). Where the config file is doesn't matter. Everything else you write seems correct to me. Let me know if this works! Good luck!

Best wishes,
Martin

sitiazma
Posts: 11
Joined: Tue Sep 15, 2009 12:29 pm

Re: REMC hippo_input

Post by sitiazma » Thu Sep 24, 2009 11:03 am

Hi

It is still not working. I have changed the filenames (the hippo_p3_mpi and also the configfile.dat to configfile. Below is the error msg, after the command

> mpiexec -configfile configfile

problem with execution of ./hippo_p3_mpi on node002: [Errno 2] No such file or directory
problem with execution of ./hippo_p3_mpi on node002: [Errno 2] No such file or directory
problem with execution of ./hippo_p3_mpi on node002: [Errno 2] No such file or directory
problem with execution of ./hippo_p3_mpi on node002: [Errno 2] No such file or director

Hope you can still suggest something. Thanks a lot.

Best regards

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: REMC hippo_input

Post by martin » Thu Sep 24, 2009 12:53 pm

Hi,

Try: /home/peptide/300/hippo_mpi_p3 instead of ./hippo_mpi_p3 for the executable and then change it for each temperature. That should work.
Please let me know if it does. Good luck!
Best wishes,
Martin

sitiazma
Posts: 11
Joined: Tue Sep 15, 2009 12:29 pm

Re: REMC hippo_input

Post by sitiazma » Thu Sep 24, 2009 1:17 pm

Hi,

I've changed to full pathway now. It seemed working because the log.txt files appear in each directory. Now the problem is as before. The log.txt files look ok, no error indication. But, the simulation is not running.

Do you need to run mpdboots? or specify any machinefile before running the mpiexec?

I hope there is still any suggestion. Thanks again.

Best regards

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: REMC hippo_input

Post by martin » Thu Sep 24, 2009 3:28 pm

Yes i think you have to run mdpboot on each node before using mpiexec.
Sorry this is so complicated. MPI is a pain!
Let me know how you fare.
Best wishes,
martin

Post Reply