AMBER Archive (2008)

Subject: Re: AMBER: Problem installing PMEMD with intel mpi, ifort

From: Robert Duke (
Date: Tue Oct 28 2008 - 20:12:17 CDT

Yes, as Ross says, this is a 10 patch, and the file "configure" changed between 9 and 10, so it would not work. The interconnect.intelmpi file was created though, and I think that SHOULD work with the 9 configure script (it was intended to be extensible like that). SO I would first just try running the 9 script (which I guess you probably did). Then I would note that the problem is with mkl really, and I would consider just not using mkl. As a further alternative, I have included the 10 configure script as an attachment (as configure.10 so you don't overwrite the original). It will probably work with 9 okay, and the mkl stuff has been fixed to be compatible with the more recent mkl releases (that is basically the problem here - intel has been changing what you have to do to build mkl, and figuring the new stuff out is not exactly straightforward).
Regards - Bob Duke
  ----- Original Message -----
  From: Rupesh Nanjunda
  Sent: Tuesday, October 28, 2008 5:07 PM
  Subject: AMBER: Problem installing PMEMD with intel mpi, ifort

   I am trying to install amber9 on intel core 2 duo CentOS 5.2 em64t system. Sander and Sander parallel installations were successful, but I get an error message during installation of pmemd using intel mpi and ifort

  "./configure linux_em64t ifort intelmpi pubfft" works ok,

   [root_at_Helix pmemd]# ./configure linux_em64t ifort intelmpi pubfft
  Intel ifort compiler found; version information:
  Version 10.1
  configure assumes Intel MKL is installed in /opt/intel/mkl/
  File config_data/fft.pubfft being used...
  File config_data/linux_em64t.ifort being used...
  File config_data/interconnect.intelmpi being used...
  configure assumes intelmpi files are in /opt/intel/impi/
  PMEMD Configurate successfully completed.

  but when I do "make install", I get the error message.

  [root_at_Helix pmemd]# make install
  __tmp_mkl_threading.c:(.text+0xea7): undefined reference to `omp_in_parallel'
  __tmp_mkl_threading.c:(.text+0xf46): undefined reference to `omp_get_max_threads'
  make[1]: *** [pmemd] Error 1
  make[1]: Leaving directory `/usr/local/apps/amber9/src/pmemd/src'
  make: *** [install] Error 2
  [root_at_Helix pmemd]#

  I used the pmemd10.patch2 as suggested, but get an error message during "patch -p0 -N < pmemd10.patch2"

  [root_at_Helix amber9]# patch -p0 -N < pmemd10.patch2
  patching file src/pmemd/config_data/interconnect.intelmpi
  patching file src/pmemd/configure
  Hunk #1 FAILED at 41.
  Hunk #2 FAILED at 391.
  2 out of 2 hunks FAILED -- saving rejects to file src/pmemd/configure.rej
  [root_at_Helix amber9]#

  Any suggestions would be greatly appreciated. Thanks in advance.


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