AMBER Archive (2009)

Subject: Re: [AMBER] Problem in test run

From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Tue Sep 29 2009 - 10:05:13 CDT

Dear sir,
I have install AmberTools as well as Amber 10.

On Tue, Sep 29, 2009 at 7:56 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> did you install Amber, or just AmberTools? AmberTools does not include
> the sander program.
>
> On Tue, Sep 29, 2009 at 10:21 AM, Kshatresh Dutta Dubey
> <kshatresh_at_gmail.com> wrote:
> > Dear all,
> >
> > I am trying installation of Amber 10 as parallel on a 64-bit linux
> machine.
> > I have installed AmberTool successfully with no any error in test run.
> But
> > when I am compilling amber10 parallel with MPICH2 it is giving error in
> test
> > run.
> > Log of make parallel is as..
> > ..................
> > ......................
> > .......................
> > .........................
> > cpp -traditional -I/usr/local/MPICH2/include -P -xassembler-with-cpp
> > -Dsecond=ambsecond -DBINTRAJ -DMPI -DUSE_MPI_IN_PLACE lesprm.f >
> _lesprm.f
> > /usr/local/MPICH2/bin/mpif90 -c -O0 -fno-range-check
> > -fno-second-underscore -o lesprm.o _lesprm.f
> > cpp -traditional -I/usr/local/MPICH2/include -P -xassembler-with-cpp
> > -Dsecond=ambsecond -DBINTRAJ -DMPI -DUSE_MPI_IN_PLACE les2prm.f >
> > _les2prm.f
> > /usr/local/MPICH2/bin/mpif90 -c -O0 -fno-range-check
> > -fno-second-underscore -o les2prm.o _les2prm.f
> > cpp -traditional -I/usr/local/MPICH2/include -P -xassembler-with-cpp
> > -Dsecond=ambsecond -DBINTRAJ -DMPI -DUSE_MPI_IN_PLACE checksz.f >
> > _checksz.f
> > /usr/local/MPICH2/bin/mpif90 -c -O0 -fno-range-check
> > -fno-second-underscore -o checksz.o _checksz.f
> > cpp -traditional -I/usr/local/MPICH2/include -P -xassembler-with-cpp
> > -Dsecond=ambsecond -DBINTRAJ -DMPI -DUSE_MPI_IN_PLACE addspace_atm1st.f
> >
> > _addspace_atm1st.f
> > /usr/local/MPICH2/bin/mpif90 -c -O0 -fno-range-check
> > -fno-second-underscore -o addspace_atm1st.o _addspace_atm1st.f
> > cd ../lib; ./Makelist ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> > make[2]: Entering directory `/usr/local/amber10/src/lib'
> > cpp -traditional -I/usr/local/MPICH2/include -P -xassembler-with-cpp
> > -Dsecond=ambsecond -DBINTRAJ -DMPI -DUSE_MPI_IN_PLACE random.f >
> _random.f
> > /usr/local/MPICH2/bin/mpif90 -c -O0 -fno-range-check
> > -fno-second-underscore -o random.o _random.f
> > make[2]: Leaving directory `/usr/local/amber10/src/lib'
> > make[2]: Entering directory `/usr/local/amber10/src/lib'
> > cpp -traditional -I/usr/local/MPICH2/include -P -xassembler-with-cpp
> > -Dsecond=ambsecond -DBINTRAJ -DMPI -DUSE_MPI_IN_PLACE mexit.f > _mexit.f
> > /usr/local/MPICH2/bin/mpif90 -c -O0 -fno-range-check
> > -fno-second-underscore -o mexit.o _mexit.f
> > make[2]: Leaving directory `/usr/local/amber10/src/lib'
> > make[2]: Entering directory `/usr/local/amber10/src/lib'
> > make[2]: `nxtsec.o' is up to date.
> > make[2]: Leaving directory `/usr/local/amber10/src/lib'
> > /usr/local/MPICH2/bin/mpif90 -o addles lesmain.o addspace.o readprm.o
> > writprm.o readcrd.o writcrd.o pick.o rline.o nxt.o intgr.o
> > find.o of.o geti.o unit.o getc.o alert.o echo.o get4c.o
> > getd.o wlesprm.o lesprm.o les2prm.o checksz.o addspace_atm1st.o
> > ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> > mv addles ../../exe
> > make[1]: Leaving directory `/usr/local/amber10/src/addles'
> >
> > Installation of Amber10 (parallel) is complete at Tue Sep 29 19:35:01 IST
> > 2009
> >
> > *
> > The log of make test is as .......*
> >
> > (find . -name '*.dif' -o -name 'profile_mpi' | \
> > while read dif ;\
> > do \
> > rm -f $dif ;\
> > done ;\
> > )
> > rm -f TEST_FAILURES.diff
> > cd dmp && ./Run.dmp
> > ../../exe/sander: Command not found.
> > ./Run.dmp: Program error
> > make: *** [test.sander.BASIC.nopar] Error 1
> >
> >
> >
> > Kindly help me for this problem...
> >
> > Thanks in advance
> > Kshatresh Dutta Dubey
> > Depart of Physics
> > DDU Gorakhpur University,Gorakhpur
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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