AMBER Archive (2008)

Subject: RE: AMBER: Installation problem of AMBER on cluster

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 02 2008 - 10:41:48 CDT

Hi Sudipta,

 

You should do the following if I remember correctly (assuming you are using
the BASH shell):

 

cd /usr/local

tar -xvzf mpich2-1.0.7.tar.gz

cd mpich2-1.0.7

export FC=g95

export F90=g95

export LDFLAGS=-all-static

export FFLAGS=-static

export CFLAGS=-static

export CXXFLAGS=-static

export CXXLDFLAGS=-static

 

(note: you may not need the last 5 options, or they may not work, but it is
useful to try since if you can build a static version it will help you later
since you will not need to worry about setting all the library paths on each
node etc.)

 

./configure -prefix=/usr/local/mpich2-1.0.7-g95

 

make

make install

 

(Then you can build the parallel version of AMBER - for amber 9)

 

export MPI_HOME=/usr/local/mpich2-1.0.7-g95/

export PATH=/usr/local/mpich2-1.0.7-g95/bin/

 

(note: the two commands above should probably be put in the default bashrc
so they get set every time you login.)

 

cd $AMBERHOME/src/

./configure -static -mpich2 g95

make clean

make parallel

 

Then you can run the parallel tests etc.

 

Good luck,

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
sudipta sinha
Sent: Friday, May 02, 2008 12:39 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation problem of AMBER on cluster

 

Dear sir,
      
          can you please help me about the compilation procedure of mpich2.
We have installed our mpich2 by the following commands.
 cd /usr/local/
 tar -zxvf mpich2-1.0.7.tar.gz
 cd mpich2-1.0.7
 ./configure
 make
 make install
 Our operating system is RHEL4 and I think the default c and fortran
compiler in RHEL4 are used during the compilation. Here we didn't set g95
compiler for the compilation of mpich2. So, please guide me how to install
mpich2 with g95 and gcc (default c compiler in RHEL4) compiler.

sudipta

On Fri, May 2, 2008 at 12:25 AM, David A. Case <case_at_scripps.edu> wrote:

On Thu, May 01, 2008, sudipta sinha wrote:
>
> make clean
>
 make: *** [clean] Error 2

So, "make clean" did not work, because there is no config.h file.
>
> ./configure -mpich2 g95

This step creates the config.h file. So, you need to do "make clean" now,
(i.e. after the configure step).

>
> MPI_HOME is set to /usr/local/

This implies that the mpich2 libraries (like libmpichf90.*) are in
/usr/local/lib. Make sure that is the case.

> evb_init.o(.data+0x460): undefined reference to `mpi_conversion_fn_null_'

It seems to have found the libraries. The most common problem here is that
the mpich2 libraries were compiled with a different fortran compiler than
g95.
Is that the case?

...good luck...dac

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