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 - 16:18:48 CDT

Hi Sudipta

Did you replace the contents of ~/.bashrc with those two exports?

You need to append these to your ~/.bashrc file. It should look something
like:

# .bashrc
# User specific aliases and functions
# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi
#default create 0700
umask 077
#CVS Specs
export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
export PATH=/usr/local/mpich2-1.0.7-g95/bin/

I suggest though that you find someone else who has a username on the
machine and see what their default .bashrc file looks like. Do you have a
system administrator? Someone who set the machine up for you?

Ross

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
sudipta sinha
Sent: Friday, May 02, 2008 1:30 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation problem of AMBER on cluster

HIi Ross,

After setting the two environment varible in .bashrc  file and compiling it
by source command
no command is working on the terminal(such as vi, scp, cp, mv etc. etc.). I
don't understand what I will do. Please tell me.

$vi .bashrc
export MPI_HOME=/usr/local/mpich2-1.0.7-g95/
export PATH=/usr/local/mpich2-1.0.7-g95/bin/  
$source .bashrc

Thank and regards
sudipta

On Sat, May 3, 2008 at 12:37 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
Hi Sudipta

This is from the log file:

configure:3475: gcc -static  -all-static conftest.c  >&5
cc1: error: unrecognized command line option "-all-static"

So that is the problem - thus try changing the export LDFLAGS=-all-static to
just -static and try again.

Good luck
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
sudipta sinha
Sent: Friday, May 02, 2008 11:30 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation problem of AMBER on cluster

Hi Ross,

          Still I am getting some error during compilation of MPICH2. Here
the issue is coming from c compiler. Now I clearly tell you what I have
done.
In .bashrc file we put the commands
export FC=g95
export F90=g95
export LDFLAGS=-all-static
export FFLAGS=-static
export CFLAGS=-static
export CXXFLAGS=-static
export CXXLDFLAGS=-static
and then compiled it by $source .bashrc
Then I untar the  file  mpich2-1.0.7.tar.gz in /usr/local and also make a
directory mpich2-1.0.7-g95 in /usr/local.  Then  I have typed  the command 
$./configure –prefix=/usr/local/mpich2-1.0.7-g95
But it is giving some errors
ERRORS:==================================================
Configuring MPICH2 version 1.0.7 with
'--prefix=/usr/local/mpich2-1.0.7-g95/' 'CFLAGS=-static' 'CXXFLAGS=-static'
'F90=g95' 'FFLAGS=-static' 'LDFLAGS=-all-static'
Running on system: Linux node3 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44 EST
2007 x86_64 x86_64 x86_64 GNU/Linux
Executing mpich2prereq in /usr/local/mpich2-1.0.7/src/mpid/ch3 with
Executing mpich2prereq in /usr/local/mpich2-1.0.7/src/mpid/ch3/channels/sock
sourcing /usr/local/mpich2-1.0.7/src/pm/mpd/mpich2prereq
sourcing /usr/local/mpich2-1.0.7/src/pm/mpd/setup_pm
checking for gcc... gcc
checking for C compiler default output file name... configure: error: C
compiler cannot create executables
See `config.log' for more details.

============================================================================
=====

I am also attaching the config.log file. Please see and tell me what is my
wrong.

Thanks and regards
sudipta
On Fri, May 2, 2008 at 9:11 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu