AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Oct 28 2008 - 19:41:39 CDT

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:

 

1) MPI_LIBS =

2) F90 = mpif90

3) LOAD = mpif90

4) LOADLIBS = /opt/intel/mkl/10.0.5.025/lib/em64t/libmkl_lapack.a
/opt/intel/mkl/10.0.5.025/lib/em64t/libmkl_em64t.a
-L/opt/intel/mkl/10.0.5.025//lib/em64t -lguide -lpthread

 

Then try building and see if that helps.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Rupesh Nanjunda
Sent: Tuesday, October 28, 2008 2:07 PM
To: amber_at_scripps.edu
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_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/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_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. 

-- 
Rupesh

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