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
>
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Received on Wed Nov 22 2006 - 23:01:46 PST
