Dear Ross,
Thanks a lot for your reply. After I entered:
cd $AMBERHOME/src
./configure -nopar xlf90_aix
make clean
make
I got message says:
#############################
cd ../lib ; ./Makelist ../lib/mexit.o ../lib/amopen.o
../lib/lapack.o
Target "mexit.o" is up to date.
Target "amopen.o" is up to date.
/lib/cpp -traditional -P
-I/hpcx/home/e39/e39/uq281/amber8/src/include -DMASSLIB -DESSL -DNMLEQ
-DCLINK_PLAIN -Drs6000 lapack.f > _lapack.f
1506-173 (W) Option traditional is not valid. Enter xlc for list of valid
options.
xlf90 -c -qfixed -c -o lapack.o _lapack.f
** dgetrf === End of Compilation 1 ===
** dgetrs === End of Compilation 2 ===
** dgetf2 === End of Compilation 3 ===
** dlaswp === End of Compilation 4 ===
** ilaenv === End of Compilation 5 ===
** lsame === End of Compilation 6 ===
** xerbla === End of Compilation 7 ===
** dgemm === End of Compilation 8 ===
** dger === End of Compilation 9 ===
** dscal === End of Compilation 10 ===
** dswap === End of Compilation 11 ===
** dtrsm === End of Compilation 12 ===
** idamax === End of Compilation 13 ===
1501-510 Compilation successful for file _lapack.f.
cd ../Machines/ibm_aix ; make sys.a
/bin/sh: ../Machines/ibm_aix: not found.
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 2.
###############################
And then continued using:
cd ../test
make clean
make
The message i got is following:
##########################
cd qmmm/standard; ./Run.lysine
exec(): 0509-036 Cannot load program ../../../exe/sander.QMMM because of the
following errors:
0509-026 System error: There is not enough memory available now.
./Run.lysine: Program error
make: 1254-004 The error code from the last command is 1.
##########################
And also if i type 'which mpxlf90' it does return to /usr/bin/mpxlf90
So any clues why is this happening? thanks a lot!
Best regards,
Rachel
On 11/22/06, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> 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
> "POE".
>
> You would typically run a parallel job setting:
>
> setenv MP_NODES 1
> setenv MP_TASKS_PER_NODE 8
> 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:
>
> cd $AMBERHOME/src
> ./configure -nopar xlf90_aix
> make clean
> make
> cd ../test
> make clean
> make
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Rachel
> *Sent:* Wednesday, November 22, 2006 02:09
> *To:* amber.scripps.edu
> *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
> following:
> ----------------------------------------------------------------------
> 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.
> Stop.
> --------------------------------------------------------------------------------------------------------
>
>
> 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 (http://www.msi.umn.edu/~cpsosa/ChemApps/MolMech/amber/patches/amber8/INSTALL_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,
> Rachel
>
>
>
> On 11/21/06, Scott Brozell <sbrozell.scripps.edu> wrote:
> >
> > Hi,
> >
> > 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_sander.f
> >
> > 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
> > http://amber.scripps.edu/doc8/errata.html
> >
> > Scott
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
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Received on Wed Nov 22 2006 - 23:01:52 PST
