AMBER Archive (2008)

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

From: Rupesh Nanjunda (rupesh.nanjunda_at_gmail.com)
Date: Thu Oct 30 2008 - 10:07:56 CDT

Not sure if my previous comments went through, so I am writing again. I was
able to solve the pmemd problem with intel mpi using the suggestions by
Robert and Ross.

First I tried Ross's suggestion.

[root_at_Helix pmemd]#*make clean* (no errors)
[root_at_Helix pmemd]#*./configure linux_em64t ifort intelmpi pubfft *(no
errors, completed successfully)

next I made the relevant changes in the config.h file

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*
saved the file and typed

[root_at_Helix pmemd]#* make install*
*
*
after a while, got a similar error message again :(

Next, I tried Robert's suggestion.
Copied the configure.10 to pmemd directory. and

[root_at_Helix pmemd]# *make clean *
[root_at_Helix pmemd]# *./configure.10* (gave me the option for intelmpi)
[root_at_Helix pmemd]# *./configure.10 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.
[root_at_Helix pmemd]# *make install* (did not give error messages. pmemd
installation was complete)

Now I have pmemd executable in the exe directory.

[rupesh_at_Helix ~]$ *pmemd*
 MPI version of PMEMD must be used with 2 or more processors!
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[rupesh_at_Helix ~]$

As you can see pmemd is running now ! The latest error can be fixed...
*configure.10
and interconnect.intelmpi did the trick*. Thank you very much Ross and
Robert for your suggestions.

happy amber user
--Rupesh

On Tue, Oct 28, 2008 at 9:12 PM, Robert Duke <rduke_at_email.unc.edu> wrote:

> 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 <rupesh.nanjunda_at_gmail.com>
> *To:* amber_at_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_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
>
> 

-- 
Rupesh

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