RE: AMBER: Problem installing PMEMD with intel mpi, ifort

From: Ross Walker <>
Date: Tue, 28 Oct 2008 17:41:39 -0700

Hi Rupesh,


PMEMD v9 has never been updated to support Intel MPI. The patch you are
referring to is only for AMBER 10. You could perhaps try to hack the
config.h file for amber9 to try to get it to work with intel mpi. You can
try the following which may work.


First run make clean


Then edit config.h and change:



2) F90 = mpif90

3) LOAD = mpif90

4) LOADLIBS = /opt/intel/mkl/
-L/opt/intel/mkl/ -lguide -lpthread


Then try building and see if that helps.


All the best



From: [] On Behalf Of
Rupesh Nanjunda
Sent: Tuesday, October 28, 2008 2:07 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.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.Helix pmemd]# make install
__tmp_mkl_threading.c:(.text+0xea7): undefined reference to
__tmp_mkl_threading.c:(.text+0xf46): undefined reference to
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/usr/local/apps/amber9/src/pmemd/src'
make: *** [install] Error 2
[root.Helix pmemd]#

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

[root.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.Helix amber9]#

Any suggestions would be greatly appreciated. Thanks in advance.

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Received on Wed Oct 29 2008 - 05:11:28 PDT
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