Re: AMBER: compiling pmemd on dual xeon

From: Robert Duke <>
Date: Tue, 17 May 2005 13:49:48 -0400

Tiziano -
Have you set 'stacksize unlimited' in your .cshrc (or done the equivalent things if you use the Bourne shell)?
Regards - Bob Duke
  ----- Original Message -----
  From: Tiziano Tuccinardi
  Sent: Tuesday, May 17, 2005 1:28 PM
  Subject: AMBER: compiling pmemd on dual xeon

  Dear all,
  I'm trying to compile amber8 on a dual Xeon 3.4 GHz using Fedora core 3, mpich-1.2.6 and intel fortrand compiler 8.1
  I hadn't any problem with the parallel version of sander, but I have some problem with pmemd:
  I use this file config.h
  #!/bin/csh -f
  setenv MPICH_HOME /usr/local/mpich-1.2.6
  setenv MPICH_INCLUDE $MPICH_HOME/include
  setenv MPILIB "-L$MPICH_LIBDIR -lmpich"


  setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"

  setenv OPT_LO "ifort -c -auto -tpp7 -O0"
  setenv OPT_MED "ifort -c -auto -tpp7 -O2"
  setenv OPT_HI "ifort -c -auto -tpp7 -xW -mp1 -ip -O3"

  setenv LOAD "ifort"
  setenv LOADLIB " -limf -lsvml $MPILIB"

  The compilation doesn't give me any error, but when I launch a calculation I have this error:

p0_31812: p4_error: interrupt SIGSEGV: 11
p1_31841: p4_error: interrupt SIGSEGV: 11

Anyone else experience something like this?

  Thanks in advanced


  Dr. Tiziano Tuccinardi
  Dip. Scienze Farmaceutiche
  Via Bonanno, 6
  56126 PISA
  Tel ++39 050 2219572

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Received on Tue May 17 2005 - 19:53:00 PDT
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