do you have any programs in the exe directory?
which commands did you use to compile amber?
On Tue, Sep 29, 2009 at 11:05 AM, Kshatresh Dutta Dubey
<kshatresh.gmail.com> wrote:
> Dear sir,
> I have install AmberTools as well as Amber 10.
>
> On Tue, Sep 29, 2009 at 7:56 PM, Carlos Simmerling <
> carlos.simmerling.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.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.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Tue Sep 29 2009 - 08:30:02 PDT
