Hi Nyla,
This problem is an apparent bug, according to Dr. Case. But it doesn't come
to bite you much. See this response earlier to a post on this community:
http://archive.ambermd.org/201003/0652.html
Try running a simple simulation and see if you're getting the expected
results.
Regards,
Ali
On Tue, Jul 26, 2011 at 2:19 PM, Nyla Zaman <nyla.zaman.hotmail.com> wrote:
>
> thankyou amir, ali and scott. the problem has been resolved. but now when i
> run a test for amber , it gives the following error.
>
> make test
> (find . -name '*.dif' -o -name 'profile_mpi' | \
> while read dif ;\
> do \
> rm -f $dif ;\
> done ;\
> )
> rm -f TEST_FAILURES.diff
> cd dmp && ./Run.dmp
> diffing mdout.dmp.save with mdout.dmp
> PASSED
> ==============================================================
> cd adenine && ./Run.adenine
> diffing mdout.adenine.save with mdout.adenine
> PASSED
> ==============================================================
> cd cytosine && ./Run.cytosine
> diffing cytosine.out.save with cytosine.out
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper
> diffing mdout.nonper.save with mdout.nonper
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.belly
> diffing mdout.belly.save with mdout.belly
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.belly.mask
> diffing mdout.belly.mask.save with mdout.belly.mask
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.min
> diffing mdout.min.save with mdout.min
> PASSED
> ==============================================================
> cd nonper && ./Run.cap
> diffing mdout.cap.save with mdout.cap
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.nocut
> diffing mdout.nocut.save with mdout.nocut
> PASSED
> ==============================================================
> cd tip4p && ./Run.tip4p
> diffing mdout.tip4p.save with mdout.tip4p
> PASSED
> ==============================================================
> cd tip4p && ./Run.tip4p_nve
> diffing mdout.tip4p_nve.save with mdout.tip4p_nve
> PASSED
> ==============================================================
> cd tip5p && ./Run.tip5p
> diffing mdout.tip5p.save with mdout.tip5p
> PASSED
> ==============================================================
> cd tip5p && ./Run.tip5p_nve
> diffing mdout.tip5p_nve.save with mdout.tip5p_nve
> PASSED
> ==============================================================
> cd 4096wat && ./Run.pure_wat
> diffing mdout.pure_wat.save with mdout.pure_wat
> PASSED
> ==============================================================
> cd 4096wat && ./Run.pure_wat_nmr_temp_reg
> diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp
> PASSED
> ==============================================================
> cd 4096wat && ./Run.vrand
> diffing mdout.vrand.save with mdout.vrand
> PASSED
> ==============================================================
> cd dhfr && ./Run.dhfr
> diffing mdout.dhfr.save with mdout.dhfr
> PASSED
> ==============================================================
> cd dhfr && ./Run.dhfr.noshake
> diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake
> PASSED
> ==============================================================
> cd dhfr && ./Run.dhfr.min
> diffing mdout.dhfr.min.save with mdout.dhfr.min
> PASSED
> ==============================================================
> cd gact_ips && ./Run.ips
> diffing mdout.ips.save with mdout.ips
> PASSED
> ==============================================================
> cd gact_ips && ./Run.ipsnve
> diffing mdout.ipsnve.save with mdout.ipsnve
> PASSED
> ==============================================================
> cd gact_ips && ./Run.ips_sgld
> diffing mdout.ips_sgld.save with mdout.ips_sgld
> PASSED
> ==============================================================
> cd polarizable_water && ./Run.pol_wat
> diffing mdout.polwat.save with mdout.polwat
> PASSED
> ==============================================================
> cd ubiquitin && ./Run.ubiquitin
> diffing mdout.ubiquitin.save with mdout.ubiquitin
> PASSED
> ==============================================================
> diffing mden.save with mden
> PASSED
> ==============================================================
> diffing mdcrd.save with mdcrd
> PASSED
> ==============================================================
> diffing mdvel.save with mdvel
> PASSED
> ==============================================================
> cd dna_pol && ./Run.dna_pol
> diffing mdout.dna_pol.save with mdout.dna_pol
> PASSED
> ==============================================================
> cd trx && ./Run.trx
> diffing mdout.trx.save with mdout.trx
> PASSED
> ==============================================================
> cd trx && ./Run.trx.cpln
> diffing mdout.trx.cpln.save with mdout.trx.cpln
> PASSED
> ==============================================================
> cd rdc && ./Run.dip
> ./Run.dip: Program error
> make: *** [test.sander.BASIC] Error 1
>
>
> > Date: Tue, 26 Jul 2011 13:43:28 +0500
> > From: alifar76.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] problem installing amber 10
> >
> > Hi Nyla,
> >
> > I was facing similar problems. As Scott has rightly said, use gfortran
> > instead of g95. It should do the trick.
> >
> > # ./configure_amber –static gfortran <enter>
> >
> > It will generate Amber configuration file (config_amber.h)
> >
> > Hope it helps!
> >
> > Regards,
> > Ali A. Faruqi
> > Karachi
> >
> > On Tue, Jul 26, 2011 at 10:33 AM, Nyla Zaman <nyla.zaman.hotmail.com>
> wrote:
> >
> > >
> > > command:
> > > ./configure_amber -static g95
> > >
> > > error:
> > > Setting AMBERHOME to /root/nyla_working/amber10
> > >
> > > Setting up Amber configuration file for architecture: g95
> > > Using parallel communications library: none
> > > The MKL_HOME environment variable is not defined.
> > >
> > > Testing the C compiler:
> > > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32 -o testp
> > > testp.c
> > > OK
> > >
> > > Testing the Fortran compiler:
> > > g95 -O0 -fno-second-underscore -o testp testp.f
> > > ./configure_amber: line 1168: g95: command not found
> > > ./configure_amber: line 1169: ./testp: No such file or directory
> > > Unable to compile a Fortran program using g95 -O0
> -fno-second-underscore
> > > Please check your compiler settings or configure flags.
> > >
> > > i tried to install g95 after that and the compiler says:
> > >
> > > ERROR:
> > >
> > > ./configure_amber -static g95
> > > Setting AMBERHOME to /root/nyla_working/amber10
> > >
> > > Setting up Amber configuration file for architecture: g95
> > > Using parallel communications library: none
> > > The MKL_HOME environment variable is not defined.
> > >
> > > Testing the C compiler:
> > > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32 -o testp
> > > testp.c
> > > OK
> > >
> > > Testing the Fortran compiler:
> > > g95 -O0 -fno-second-underscore -o testp testp.f
> > > g95: installation problem, cannot exec 'f951': No such file or
> directory
> > > ./configure_amber: line 1169: ./testp: No such file or directory
> > > Unable to compile a Fortran program using g95 -O0
> -fno-second-underscore
> > > Please check your compiler settings or configure flags.
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 26 2011 - 04:00:03 PDT
