Dear all:
We are trying to install Amber8 on our PC-cluster with athlon platform,
MPICH and compiler ifort and have finished the compiling works; however,
when testing parallel works, something very strange happened. I issue
the steps of compiling and problems in my test works here:
Setenv AMBERHOME /user/local/amber8
Setenv MPICH_HOME /user/local.....
../configure -athlon -static ifort
Make serial
Make test.<programme-name>
Make clean
../configure -mpich -static ifort
Make parallel
At the end of the compiling, the machine told me everything was ok and
the single threaded works passed the test smoothly. But when I did
these:
Cd /AMBERHOME/test
Setenv DO_PARALLEL "mpirun -np 4" (or "/user/local/mpich_ifc/bin/mpirun
-np 4)
Make test.parallel
The machine told me like this:
[nnizb.nemo test]$ make test.parallel
make: *** No rule to make target `test.parallel'. Stop.
When I test one of my works, I issued command like these:
[nnizb.nemo test]$ mpirun -np 4 sander -O -i 888.in -p 888.parm -c
888.crd -o 888.out -r 888.rst
or
[nnizb.nemo test]$ /user/local/mpich_ifc/bin/mpirun -np 4 sander -O -i
888.in -p 888.parm -c 888.crd -o 888.out -r 888.rst
And the error messages were given like:
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_12768: p4_error: : 1
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Our OS is npaci rocks 3.3 linux (it is based on Redhat linux and very
very similar with Redhat linux).
We also failed when we tried to install amber8 on another cluster. The
administrator told us that was due to the lack of MPI library on each
node, so he has to install the library on each node. Is this true? Do
you need to do this before you install amber on your machine?
Thank you!
Zhang Bing
National University of Singapore
Nanoscience and Nanotechnology Initiative
nnizb.nus.edu.sg
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Received on Thu Jun 02 2005 - 07:53:03 PDT
