AMBER Archive (2006)

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

From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Nov 22 2006 - 04:08:42 CST

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_at_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
>
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