AMBER Archive (2003)

Subject: AMBER: Scyld cluster amber 7 compile problems

From: Bengt Svensson (bsven_at_msi.umn.edu)
Date: Wed Sep 17 2003 - 20:11:04 CDT

I have been trying to install Amber 7 on a Sculd Linux cluster, but are
having some problems.

The cluster is 4 dual AMD Athlon MP 2600+ (total 8 cpu), 2GB memory
per node, with gigabit ethernet connection.
It is running Scyld 28cz5.1 (Based off RedHat 7.1?), gcc 2.96, pgf77 5.0-2,
and mpich 1.2.3.

The source code for amber 7 has been patched with bugfix 1-39.

I have followed the instruction and used the Machine files from:

http://amber.scripps.edu/cluster_info/index.html

I did the following modifications to reflect the location of the MPICH
libraries and SYSDIR

#setenv MPICH_HOME /usr/lib/mpich
setenv MPICH_HOME /usr

#setenv SYSDIR Machines/g77
setenv SYSDIR Machines/standard

I tried both to compile with pgf77 and g77, serial and parallel (mpi)
versions.

When I compile with pgf77 everything seems to be going fine. No warnings.

I run the test.sander and I get errors on the following tests (see below).
Most tests ran just fine. This happened with both the serial and
parallel versions.

Compilation with g77 gives quite a few warnings, but completes.
test.sander works just fine, all tests are passed.

What is the cause of these errors with pgf77? Do anyone have any
suggestions?

Thanks,

        Bengt Svensson

***pgf77 serial***

cd tgtmd/change_target; ./Run.tgtmd
SANDER: Targeted MD with changing target
PGFIO-F-225/namelist read/unit=5/lexical error-- unknown token type.
 File name = tgtmd.in formatted, sequential access record = 16
 In source file _restal_.f, at line number 142
  Program error
make: *** [test.sander] Error 1

***pgf77 parallel (mpich)***

cd tgtmd/change_target; ./Run.tgtmd
SANDER: Targeted MD with changing target
PGFIO-F-225/namelist read/unit=5/lexical error-- unknown token type.
 File name = tgtmd.in formatted, sequential access record = 16
 In source file _restal_.f, at line number 142
p3_2705: p4_error: net_recv read: probable EOF on socket: 1
p2_2703: p4_error: net_recv read: probable EOF on socket: 1
p1_2702: p4_error: net_recv read: probable EOF on socket: 1
bm_list_2701: (0.140309) net_send: could not write to fd=5, errno = 9
bm_list_2701: p4_error: net_send write: -1
    p4_error: latest msg from perror: Bad file descriptor
  Program error
make: *** [test.sander] Error 1

cd tgtmd/PME; ./Run.tgtPME
SANDER: Targeted MD with PME
PGFIO-F-225/namelist read/unit=5/lexical error-- unknown token type.
 File name = tgtmd.in formatted, sequential access record = 23
 In source file _restal_.f, at line number 142
p3_4277: p4_error: net_recv read: probable EOF on socket: 1
p2_4275: p4_error: net_recv read: probable EOF on socket: 1
p1_4274: p4_error: net_recv read: probable EOF on socket: 1
bm_list_4273: (0.141386) net_send: could not write to fd=5, errno = 9
bm_list_4273: p4_error: net_send write: -1
    p4_error: latest msg from perror: Bad file descriptor
  Program error
make: *** [test.sander] Error 1

------------------------------------------------------------------------------
  Dr. Bengt Svensson
  University Of Minnesota e-mail: bsven_at_msi.umn.edu
  Dept. of Medicinal Chemistry tel: +1-612-626-4429
  8-101 Weaver-Densford Hall fax: +1-612-626-4429
  308 Harvard St. SE
  Minneapolis, MN 55455
  USA Visiting addr: 7-125D Weaver-Densford Hall

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