AMBER Archive (2005)

Subject: AMBER: amber8 installation problems

From: Zhang Bing (nnizb_at_nus.edu.sg)
Date: Thu Jun 02 2005 - 01:55:48 CDT

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_at_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_at_nemo test]$ mpirun -np 4 sander -O -i 888.in -p 888.parm -c
888.crd -o 888.out -r 888.rst

 

or

 

[nnizb_at_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_at_nus.edu.sg

 

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