Payman Pirzadeh wrote:
Hi Justin,
Since the manual itself was not sufficient, I asked some other people who
are running GROMACS in our group (but they run only on 2 CPUs). Here are the
steps I took to compile the parallel version (I have included my notes that
they told me as well):
Installation
1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4
This line specifies the installation path
2. Make
3. Make install
These two commands will make 'grompp' and analysis functions of GROMACS.
4. Make clean
This command will clean some files generated during installation which are
not needed anymore.
5. ./configure --enable-mpi --disable-nice
--prefix=/global/home/pirzadeh/gromacs-4.0.4
Here we compile the code for parallel version of GROMACS
6. make mdrun
7. make install-mdrun
Now the parallel version of mdrun is built. The analysis functions are found
in 'bin' folder accompanied by 'GMXRC'.
8. Before running 'grompp' to produce the topology file for simulation,
we should use the command source
/global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the
current code.
This is pretty much the standard installation procedure. What we also need to
know are the compilers used, etc. for the installation. The error you're
getting is from MPICH. Which version is installed on the cluster? It may be
old and buggy. In any case, you can try to install something newer, like a
recent version of OpenMPI (which we have on our cluster); it may be more
reliable. Only a random thought, means nothing unless we know what you have
installed :)
What about the contents of your system, as I asked before? Do you really have a
100% virtual site system?
-Justin
Sorry for tons of e-mails.
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: June 8, 2009 11:12 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote:
Hi,
I had the chance to run the GROMACS 4.0.4 on another cluster. Same
problem still persists. But what I found is that it can be run on a node
with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, .
it will crash. Following are the last lines reported in different files:
"In the log file of the code":
There are: 1611 Atoms
There are: 1611 VSites
All of your atoms are virtual sites? If so, I would try a simpler test
case, to
rule out stumbling across some obscure bug.
Also:
p2_22627: p4_error: Timeout in establishing connection to remote process:
0
This is an error message from MPICH, not Gromacs. See, for example:
http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html
<snip>
To me, it seems that code can not communicate through more than one
node. I am suspicious of doing sth wrong during installation! I tried
wiki, but I can not find the documents as before, and I eally do not
know in which step I might have gone wrong.
If you suspect you have done something wrong, then post the details of the
system configuration (hardware, compilers, OS, etc.) as well as a
step-by-step
record of what you did to compile the software. If your procedure is sound,
then it helps rule out the possibility that you messed something up.
-Justin
Payman
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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