Is there a UPEX version with no scp, ssh, sftp included?

[vahid]

Dear USPEX Users,

I noticed in the submitJob.m and checkStatus.m files a significant
number of scp, ssh, sftp etc. commands. Before starting to
significantly edit these files, does anyone have a version of USPEX in
which there is no local/supercomputer involved, where you simply log
onto a grid engine to submit your job and there is no need for file
transfer.

Thanks,
Vahid

[Andriy Lyakhov]

Hello,

can you tell me what exactly do you want to do? If you want to run the
USPEX without scp/sftp/ssh you just have to use local regime. But for
this your grid needs matlab (or octave). If there is no matlab on your
supercomputer, then this is impossible. Because USPEX requires matlab,
if you start USPEX on local machine it generates input files for VASP
(or other code) on local machine and you HAVE to copy them to
supercomputer to do calculations.

If your supercomputer has matlab or octave - just start USPEX there
and there will be no ssh/sftp/scp involved.

Sincerely,
Andriy

[vahid]

Hi Andriy,

I have an account on a linux cluster called Mahone (part of ACEnet).
Octave is already installed on Mahone. I have installed USPEX on my
home directory on Mahone. The code runs fine but it ssh's Mahone every
time the code restarts (via crontab or manually). I am using
remoteregime=2 with a script written manually and stored in the
RemoteSubmission folder. I did remove the following lines from the
checkStatus.m as you suggested:

try
[a,b]=unix(['scp ' portNbig EXE_STRUC.userName '@'
EXE_STRUC.serverName ':' EXE_STRUC.remoteFolder ORG_STRU
C.remoteFolder '/CalcFold'
num2str(POP_STRUC.POPULATION(Ind_No).Folder) '/output-log ./'])
end
try
[a,b]=unix(['scp ' portNbig EXE_STRUC.userName '@'
EXE_STRUC.serverName ':' EXE_STRUC.remoteFolder ORG_STRU
C.remoteFolder '/CalcFold'
num2str(POP_STRUC.POPULATION(Ind_No).Folder) '/OUTCAR ./'])
end
try
[a,b]=unix(['scp ' portNbig EXE_STRUC.userName '@'
EXE_STRUC.serverName ':' EXE_STRUC.remoteFolder ORG_STRU
C.remoteFolder '/CalcFold'
num2str(POP_STRUC.POPULATION(Ind_No).Folder) '/CONTCAR ./'])
end

but then USPEX tries to ssh Mahone. So every 5 minutes (if I use the
cron), an ssh connection opens to Mahone.

All I want to do is to be able to submit a job from my home directory
on Mahone to Mahone's queue system without having the need for any ssh
or other file transfer programs. If my explanation is unclear, please
let me know.

Many thanks,
Vahid

[Andriy Lyakhov]

Hello,

you don't have to use remote = 2 if you start USPEX on Mahone. But of
course you may do it, if you modify the files. There are actually 3
ways of using USPEX on Mahone:

1. Use remote = 0 with nonParallel regime. It will be slow but it
should work. However if you want parallel calculations (a few
structures in the same time), choose one of the following.
2. Keep remote = 2, but modify the submitJob.m and checkStatusC.m
files ('elseif ORG_STRUC.remote == 2' part) to replace ssh, sptf, scp
commands by local versions. For example in checkStatusC.m in addition
to deleting the lines that you did, replace:
[a,statusStr] = unix(['ssh ' EXE_STRUC.userName '@'
EXE_STRUC.serverName portNsmall ' ' doneCommand]);
by
[a,statusStr] = unix(doneCommand);
3. Use remote = 0 with regime Mars and modify the files submitJob.m
and checkStatusC.m ('elseif ORG_STRUC.Mars' part) as described in the
manual. This is probably the best way to do it.

Sincerely,
Andriy

[vahid]

Hi Andriy,

I used the third option you suggested and now the code runs with no
errors. Many thanks for your patience and suggestions.

Vahid