AMBER Archive (2009)

Subject: Re: [AMBER] Problem in test run

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 29 2009 - 09:26:38 CDT

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
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber