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
To: amber.scripps.edu
Sent: Tuesday, October 28, 2008 5:07 PM
Subject: AMBER: Problem installing PMEMD with intel mpi, ifort
Hi,
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/10.0.5.025
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/3.2.0.011.
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 `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.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.
--
Rupesh
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Received on Wed Oct 29 2008 - 05:11:29 PDT
