Dear David,
Thank you very much for your response!
First, I've repeated parallel installation, without -DREM:
cd AMBERHOME/src
setenv MPICH_HOME '/usr/local/mpich-intel'
make clean
../configure -mpich ifc7
make parallel
I've got the message telling that installation of Amber (parallel) is complete.
Then, I tried to test parallel AMBER8 installation. I did the following:
cd /usr/local/amber8/test
make test.sander
I've got the following:
ionia01 amber8/test# make test.sander
cd dmp; ./Run.dmp
This set not set up for parallel
cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This set not set up for parallel
cannot run in parallel with #residues < #pes
==========================================================
cd cytosine; ./Run.cytosine
2 - MPI_BCAST : Message truncated
[2] Aborting program !
[2] Aborting program!
p2_3013: p4_error: : 14
Broken pipe
Broken pipe
diffing cytosine.out.save with cytosine.out
possible FAILURE: check cytosine.out.diff
===========================================================
cd nonper; ./Run.nonper
2 - MPI_BCAST : Message truncated
[2] Aborting program !
[2] Aborting program!
p2_3091: p4_error: : 14
Broken pipe
Broken pipe
diffing mdout.nonper.save with mdout.nonper
possible FAILURE: check mdout.nonper.diff
===============================================
cd nonper; ./Run.nonper.belly
2 - MPI_BCAST : Message truncated
[2] Aborting program !
[2] Aborting program!
p2_3169: p4_error: : 14
Broken pipe
Broken pipe
diffing mdout.belly.save with mdout.belly
possible FAILURE: check mdout.belly.diff
===============================================
................................................
The rest of test resulted in similar messages.
Further, I tried to run usual job like the following:
bsub -o lsf33.log -n 18 sander -O -i 4.in -o 4.out -p 1.prmtop -c 3.rst -r 4.rst -x 4.mdcrd
and this is working.
However, when I tried to run usual simulation with the following command:
mpirun -np 18 sander -O -i 4.in -o 4.out -p 1.prmtop -c 3.rst -r 4.rst -x 4.mdcrd
I've got the following:
Warning: Command line arguments for program should be given
after the program name. Assuming -O is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming -i is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming 4.in is a
command line argument for the program.
................................................
................................................
................................................
Program sander either does not exist, is not
executable, or is an erroneous argument to mpirun.
Maybe the problem is in MPI?
I have intel fortran compiler version 7.1, gcc version 2.95.3, SuSE Linux 7.3 (i386) - Kernel 2.4.24.
I would be gratefull for any help.
Best regards,
Sergey
-----Original Message-----
From: "David A. Case" <case.scripps.edu>
To: amber.scripps.edu
Date: Tue, 29 Nov 2005 09:40:18 -0800
Subject: Re: AMBER: AMBER compilation with -DREM
>
> On Tue, Nov 29, 2005, Sergey Krishtal wrote:
> >
> > In both cases, I've got the message: "Installation of Amber (parallel)
> > completed". However, when I tried to run REMD simulations, I've got the
> > following: "mdfil: Error unknown flag: -rem".
>
> First, make sure that mdfil (and the rest of the code) is really getting
> compiled with the -DREM flag. Look at _mdfil.f for example, and look for the
> "-rem" string.
>
> Second, (if that doesn't solve it), please post the command line you are using
> to invoke this.
>
> [I'm assuming that you have downloaded the replica exchange test suite from
> the Amber web site, and that your system passes the tests. If you haven't
> done this step, please do so, and report the results.]
>
> ....good luck....dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 30 2005 - 11:53:01 PST
