AMBER Archive (2008)

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

From: Rupesh Nanjunda (
Date: Tue Oct 28 2008 - 16:07:01 CDT

 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
__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_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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