AMBER Archive (2006)

Subject: RE: AMBER: compile amber8 on IBM-sp4

From: Ross Walker (
Date: Wed Nov 22 2006 - 11:55:45 CST

Dear Rachel,
The fact that you are seeing the error:
mpirun: Command not found.

I part of your problem. On IBM Power 4 machines running AIX (I assume you
are running AIX) one typically uses IBM's parallel operating environment
You would typically run a parallel job setting:
setenv MP_NODES 1
poe $AMBERHOME/exe/sander.MPI -O blah blah blah
poe reads the environment variables to determine the number of cpus to use
rather than using a -np x option like mpirun would.
Thus to run the parallel test cases in amber9 you would set the above
environment variables to the combination of nodes and tasks you want and
then run:
setenv DO_PARALLEL poe
make test.sander.parallel
However, I believe the main issue you are having is with compiling and from
your earlier emails this seemed to be an issue with the mpi installation:
#include file "mpif.h" not found.

This could come from two situations. Firstly IBM's mpi might never have been
installed on your machine or secondly your environment variables might not
be configured correctly.
Try 'which mpxlf90' and see if it returns /usr/bin/mpxlf90
if it says 'mpxlf90: Command not found.' then I suspect mpi is not installed
or possibly installed in a non standard place. Check with whoever setup the
machine to find out which mpi they installed and where.
For the moment you should be able to build and test the serial version. I
would advise you to do this first to make sure things are working. Do:
./configure -nopar xlf90_aix
make clean
cd ../test
make clean
All the best
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | 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: [] On Behalf Of
Sent: Wednesday, November 22, 2006 02:09
Subject: Re: AMBER: compile amber8 on IBM-sp4

Hi, Scott,
Thanks very much for your reply, however, i am still not clear how to solve
the problem, you suggested to use 'make -n'? and the results are as
        cd dmp; ./Run.dmp
        cd adenine; ./Run.adenine
        cd cytosine; ./Run.cytosine
        cd nonper; ./Run.nonper
        cd nonper; ./Run.nonper.belly
        cd nonper; ./Run.nonper.belly.mask
        cd nonper; ./Run.nonper.min
        cd nonper; ./Run.cap
        cd nonper; ./Run.nonper.nocut
        cd tip4p; ./Run.tip4p
        cd tip5p; ./Run.tip5p
        cd 4096wat; ./Run.pure_wat
        cd dhfr; ./Run.dhfr
        cd dhfr; ./Run.dhfr.noshake
        cd dhfr; ./Run.dhfr.min
        cd gb_rna; ./Run.gbrna
        cd gb_rna; ./Run.gbrna.min
        cd gb_rna; ./Run.gbrna.ln
        cd gbsa_xfin; ./Run.gbsa
        cd polarizable_water; ./Run.pol_wat
        cd ubiquitin; ./Run.ubiquitin
        cd dna_pol; ./Run.dna_pol
        cd aspash; ./Run.aspash
        cd circ_dna; ./Run.circdna
        cd gb2_trx; ./Run.trxox
        cd trx; ./Run.trx
        cd trx; ./Run.trx.cpln
        cd cnstph; ./Run.cnstph
        cd rdc; ./Run.dip
        cd tgtmd/change_target; ./Run.tgtmd
        cd tgtmd/change_target.rms; ./Run.tgtmd
        cd tgtmd/change_target.ntr; ./Run.tgtmd
        cd tgtmd/conserve_ene; ./Run.tgtmd
        cd tgtmd/minimize; ./Run.tgtmin
        cd tgtmd/PME; ./Run.tgtPME
        cd trajene; ./Run.trajene
        cd pheTI; ./Run.0; ./Run.1; ./Run.p0; ./Run.p1
        cd ion_wat; ./Run.ion_wat
        cd alp; ./Run.alp
        cd pb_pgb; ./Run.pbpgb
        cd umbrella; ./Run.umbrella
        cd LES_noPME; ./Run.LESmd
        cd LES_noPME; ./Run.LESmd.rdiel
        cd LES; ./Run.PME_LES
        cd LES_CUT; ./Run.LES
        cd LES_TEMP; ./Run.2temp
        cd LES_GB; ./Run.LES
make: 1254-002 Cannot find a rule to create target \ from dependencies.
As you said the compilation line is broken, how can I make sure i provided
enough details? and if i use 'make test.sander', etc. instead of make
test.parallel, then i got:
 cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
        cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
        cd cytosine; ./Run.cytosine
mpirun: Command not found.
  ./Run.cytosine: Program error
make: 1254-004 The error code from the last command is 1.
This is the first time I compile amber myself, and as it is IBM-SP4 machine,
so what i did was just follow Carlos Sosa's Running Amber on IBM systems (
_ibm) on AMBER website, I really appreciate your help if anyone can let me
know some more details of how to do it.
Best regards,

On 11/21/06, Scott Brozell <> wrote:


On Tue, 21 Nov 2006, Rachel wrote:

> Dear all,
> I am trying to compile amber8 on the IBM-SP4 machines, I used './configure

> -mpi xlf90_aix', after i used 'make paralle', i got the following error
> message:

> "egb.f", line 131.12: 1506-296 (S) #include file "mpif.h" not found.
> make: 1254-004 The error code from the last command is 1.

It looks like the compilation line is broken.
You didn't provide enough detail, so the full command
invoked by make is not clear.

make should be invoking something like, eg

  /lib/cpp -traditional -I/usr/lpp/ppe.poe/include -P
-I/usr/local/srb/9/src/include -DMPI -DNMLEQ -DCLINK_PLAIN -Drs6000 -DPOE
sander.f > _sander.f
  mpxlf90_r -bmaxdata:0x80000000 -c -qfixed -c -qfree -o sander.o

Compare this with the output of make -n
What happens if you enter mpxlf90_r -show -help ?

> and then if i go to the $AMBERHOME/test directory and use 'make
> test.parallel', it says:

See page 7 errata


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to