AMBER Archive (2009)

Subject: Re: [AMBER] Problem in test run

From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Tue Sep 29 2009 - 10:14:35 CDT

In the exe directory ..
acdoctor bondtype matextract mopac new2oldparm rdparm
sander.LES.MPI top2mol2 tss_next
addles charmmgen matgen mopac.sh parmcal reduce
sander.MPI transform ucpp
am1bcc database matmerge nab parmchk residuegen
sleap translate xaLeap
antechamber espgen matmul nab2c prepgen resp
teLeap tss_init xleap
atomtype lmodprmtop mdout ncdump ptraj respgen
tleap tss_main yacc

are available.

I used commands
 ./configure_amber -mpich2 gfortran

for installation of Amber10 and then

 make parallel

to compile them parallel.

On Tue, Sep 29, 2009 at 8:36 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> 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_at_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_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
> >> >
> >>
> >> _______________________________________________
> >> 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
> >
>
> _______________________________________________
> 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