AMBER Archive (2009)

Subject: Re: [AMBER] Is it taking too much time

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Mon Nov 02 2009 - 23:35:04 CST

Dear Nicolas,
                   After reading the manual I have tried to install the
parallel version in my machine again. But first of all I want you to know
that we have purchased the AMBER 9 for one node user. So are you sure that
it will run in a parallel version? I have installed the mpi through
yum-extender. After that I have done the following with following errors
massages. Please help me. I am unble to understand what to do.

$cd $AMBERHOME/src

$make clean
cd lib; make clean
make[1]: Entering directory `/usr/local/amber9/src/lib'
/bin/rm malloc_test new2oldparm *.o _*.f *.a
/bin/rm: cannot remove `malloc_test': No such file or directory
/bin/rm: cannot remove `new2oldparm': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/lib'
cd blas; make clean
make[1]: Entering directory `/usr/local/amber9/src/blas'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o blas.a _*.f
make[1]: Leaving directory `/usr/local/amber9/src/blas'
cd lapack; make clean
make[1]: Entering directory `/usr/local/amber9/src/lapack'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o lapack.a _*.f
make[1]: Leaving directory `/usr/local/amber9/src/lapack'
cd lmod; make clean
make[1]: Entering directory `/usr/local/amber9/src/lmod'
/bin/rm -f *.a
cd xmin; make clean
make[2]: Entering directory `/usr/local/amber9/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f ieee.o xmin.o _*.f
make[2]: Leaving directory `/usr/local/amber9/src/lmod/xmin'
cd lmod; make clean
make[2]: Entering directory `/usr/local/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
../../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f ieee.o lmod.o _*.f
make[2]: Leaving directory `/usr/local/amber9/src/lmod/lmod'
make[1]: Leaving directory `/usr/local/amber9/src/lmod'
cd arpack; make clean
make[1]: Entering directory `/usr/local/amber9/src/arpack'
Makefile:7: warning: overriding commands for target `.f.o'
../config.h:82: warning: ignoring old commands for target `.f.o'
/bin/rm -f *.o _*.f arpack.a
make[1]: Leaving directory `/usr/local/amber9/src/arpack'
cd addles; make clean
make[1]: Entering directory `/usr/local/amber9/src/addles'
/bin/rm *.o _*.f addles
/bin/rm: cannot remove `addles': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/addles'
cd sander; make clean
make[1]: Entering directory `/usr/local/amber9/src/sander'
/bin/rm sander sander.LES psander sander.PIMD
/bin/rm: cannot remove `sander': No such file or directory
/bin/rm: cannot remove `sander.LES': No such file or directory
/bin/rm: cannot remove `psander': No such file or directory
/bin/rm: cannot remove `sander.PIMD': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm ambmask
/bin/rm: cannot remove `ambmask': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.o
/bin/rm _*.f
/bin/rm *.mod
/bin/rm *.d
/bin/rm: cannot remove `*.d': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *nbflag
/bin/rm: cannot remove `*nbflag': No such file or directory
make[1]: [clean] Error 1 (ignored)
cd ../dcqtp; make clean
make[2]: Entering directory `/usr/local/amber9/src/dcqtp'
cd mod; make clean
make[3]: Entering directory `/usr/local/amber9/src/dcqtp/mod'
rm -f ../dcqtp *.mod
rm -f ../src/qmmm/libdivcon.a
cd ../obj; rm -f *.o *.f
make[3]: Leaving directory `/usr/local/amber9/src/dcqtp/mod'
make[2]: Leaving directory `/usr/local/amber9/src/dcqtp'
make[1]: Leaving directory `/usr/local/amber9/src/sander'
cd dcqtp; make clean
make[1]: Entering directory `/usr/local/amber9/src/dcqtp'
cd mod; make clean
make[2]: Entering directory `/usr/local/amber9/src/dcqtp/mod'
rm -f ../dcqtp *.mod
rm -f ../src/qmmm/libdivcon.a
cd ../obj; rm -f *.o *.f
make[2]: Leaving directory `/usr/local/amber9/src/dcqtp/mod'
make[1]: Leaving directory `/usr/local/amber9/src/dcqtp'
cd ptraj; make clean
make[1]: Entering directory `/usr/local/amber9/src/ptraj'
cd pdb; make clean
make[2]: Entering directory `/usr/local/amber9/src/ptraj/pdb'
rm -f pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o
libpdb.a
make[2]: Leaving directory `/usr/local/amber9/src/ptraj/pdb'
/bin/rm -f main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o
experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o rdparm ptraj
/bin/rm _*.f
make[1]: Leaving directory `/usr/local/amber9/src/ptraj'
cd nmr_aux; make clean
make[1]: Entering directory `/usr/local/amber9/src/nmr_aux'
cd prepare_input; make clean
make[2]: Entering directory `/usr/local/amber9/src/nmr_aux/prepare_input'
/bin/rm *.o _*.f makeDIST_RST makeANG_RST makeSHF.cp makeCHIR_RST.cp \
        makeDIP_RST.protein.cp makeDIP_RST.dna.cp
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `makeDIST_RST': No such file or directory
/bin/rm: cannot remove `makeANG_RST': No such file or directory
/bin/rm: cannot remove `makeSHF.cp': No such file or directory
/bin/rm: cannot remove `makeCHIR_RST.cp': No such file or directory
/bin/rm: cannot remove `makeDIP_RST.protein.cp': No such file or directory
/bin/rm: cannot remove `makeDIP_RST.dna.cp': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/nmr_aux/prepare_input'
cd fantasian; make clean
make[2]: Entering directory `/usr/local/amber9/src/nmr_aux/fantasian'
/bin/rm *.o _*.f fantasian
/bin/rm: cannot remove `fantasian': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/usr/local/amber9/src/nmr_aux/fantasian'
make[1]: Leaving directory `/usr/local/amber9/src/nmr_aux'
cd nmode; make clean
make[1]: Entering directory `/usr/local/amber9/src/nmode'
/bin/rm *.o _*.f nmode nmanal
/bin/rm: cannot remove `nmode': No such file or directory
/bin/rm: cannot remove `nmanal': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/nmode'
cd resp; make clean
make[1]: Entering directory `/usr/local/amber9/src/resp'
/bin/rm *.o _*.f resp reformat replace_charges
/bin/rm: cannot remove `resp': No such file or directory
/bin/rm: cannot remove `reformat': No such file or directory
/bin/rm: cannot remove `replace_charges': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/resp'
cd protonate; make clean
make[1]: Entering directory `/usr/local/amber9/src/protonate'
/bin/rm *.o _*.f pol_h protonate gwh
/bin/rm: cannot remove `pol_h': No such file or directory
/bin/rm: cannot remove `protonate': No such file or directory
/bin/rm: cannot remove `gwh': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/protonate'
cd etc; make clean
make[1]: Entering directory `/usr/local/amber9/src/etc'
/bin/rm *.o _*.f ambpdb nucgen elsize
/bin/rm: cannot remove `ambpdb': No such file or directory
/bin/rm: cannot remove `nucgen': No such file or directory
/bin/rm: cannot remove `elsize': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/etc'
cd antechamber; make clean
make[1]: Entering directory `/usr/local/amber9/src/antechamber'
rm -f *.o am1bcc antechamber atomtype bondtype charmmgen crdgrow database
espgen parmcal parmchk prepgen respgen top2mol2 translate
make[1]: Leaving directory `/usr/local/amber9/src/antechamber'
cd mm_pbsa; make clean
make[1]: Entering directory `/usr/local/amber9/src/mm_pbsa'
/bin/rm *.o _*.f make_crd_hg molsurf
/bin/rm: cannot remove `make_crd_hg': No such file or directory
/bin/rm: cannot remove `molsurf': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/mm_pbsa'
cd pbsa; make clean
make[1]: Entering directory `/usr/local/amber9/src/pbsa'
/bin/rm pbsa
/bin/rm: cannot remove `pbsa': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.o
/bin/rm _*.f
/bin/rm *.mod
/bin/rm *.d
/bin/rm: cannot remove `*.d': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/pbsa'
cd anal; make clean
make[1]: Entering directory `/usr/local/amber9/src/anal'
/bin/rm *.o _*.f anal
/bin/rm: cannot remove `anal': No such file or directory
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory `/usr/local/amber9/src/anal'
cd leap; make clean
make[1]: Entering directory `/usr/local/amber9/src/leap'
cd src/Wc; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Wc'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Wc'
cd src/Xmu; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Xmu'
Makefile:122: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Xmu'
cd src/Xpm; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Xpm'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Xpm'
cd src/Xraw; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/Xraw'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o *.a
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Xraw'
cd src/leap; make clean
make[2]: Entering directory `/usr/local/amber9/src/leap/src/leap'
Makefile:4: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
/bin/rm *.o xaLeap teLeap utilMakeHelp utilDescribeTopology utilCrd2Off
mol2_to_off utilConvertWaterBox utilLib2Pdb *\~
/bin/rm: cannot remove `xaLeap': No such file or directory
/bin/rm: cannot remove `teLeap': No such file or directory
/bin/rm: cannot remove `utilDescribeTopology': No such file or directory
/bin/rm: cannot remove `utilCrd2Off': No such file or directory
/bin/rm: cannot remove `mol2_to_off': No such file or directory
/bin/rm: cannot remove `utilConvertWaterBox': No such file or directory
/bin/rm: cannot remove `utilLib2Pdb': No such file or directory
/bin/rm: cannot remove `*~': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm XaLeap_wcl
/bin/rm: cannot remove `XaLeap_wcl': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm *.gprof
/bin/rm: cannot remove `*.gprof': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm parser.c
/bin/rm helptext.c
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/leap'
make[1]: Leaving directory `/usr/local/amber9/src/leap'
cd pmemd; make clean
make[1]: Entering directory `/usr/local/amber9/src/pmemd'
cd src && rm -f *.f90 *.o *.mod pmemd *.d work.pc*
make[1]: Leaving directory `/usr/local/amber9/src/pmemd'
cd build_amoeba; make clean
make[1]: Entering directory `/usr/local/amber9/src/build_amoeba'
/bin/rm amoeba_parm new_crd_to_dyn new_to_old_crd
/bin/rm: cannot remove `amoeba_parm': No such file or directory
/bin/rm: cannot remove `new_crd_to_dyn': No such file or directory
/bin/rm: cannot remove `new_to_old_crd': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm amoeba_parm.f new_crd_to_dyn.f new_to_old_crd.f fix_new_inpcrd_vel.f
/bin/rm: cannot remove `fix_new_inpcrd_vel.f': No such file or directory
make[1]: [clean] Error 1 (ignored)
/bin/rm *.o
/bin/rm *.mod
make[1]: Leaving directory `/usr/local/amber9/src/build_amoeba'
cd netcdf/src; make clean
make[1]: Entering directory `/usr/local/amber9/src/netcdf/src'
Makefile:4: macros.make: No such file or directory
rules.make:118: warning: overriding commands for target `/'
Makefile:173: warning: ignoring old commands for target `/'
rules.make:120: warning: overriding commands for target `/'
rules.make:118: warning: ignoring old commands for target `/'
rules.make:122: warning: overriding commands for target `/'
rules.make:120: warning: ignoring old commands for target `/'
rules.make:124: warning: overriding commands for target `/'
rules.make:122: warning: ignoring old commands for target `/'
rules.make:127: warning: overriding commands for target `/'
rules.make:124: warning: ignoring old commands for target `/'
rules.make:130: warning: overriding commands for target `/'
rules.make:127: warning: ignoring old commands for target `/'
rules.make:145: warning: overriding commands for target `/man1'
rules.make:142: warning: ignoring old commands for target `/man1'
rules.make:147: warning: overriding commands for target `/man3'
rules.make:142: warning: ignoring old commands for target `/man3'
rules.make:150: warning: overriding commands for target `/man3f'
rules.make:142: warning: ignoring old commands for target `/man3f'
rules.make:154: warning: overriding commands for target `/man3f90'
rules.make:142: warning: ignoring old commands for target `/man3f90'
make[1]: *** No rule to make target `macros.make'. Stop.
make[1]: Leaving directory `/usr/local/amber9/src/netcdf/src'
make: [clean] Error 2 (ignored)
cd netcdf/lib && rm -f libnetcdf.a
/bin/sh: line 0: cd: netcdf/lib: No such file or directory
make: [clean] Error 1 (ignored)
cd netcdf/include && rm -f *.mod
/bin/sh: line 0: cd: netcdf/include: No such file or directory
make: [clean] Error 1 (ignored)

$./configure -mpi ifort_ia32
AMBERHOME is set to /usr/local/amber9
Setting up Amber configuration file for architecture: ifort_ia32
Using parallel communications library: mpi
The MKL_HOME environment variable is not defined.
    The MKL is recommended for optimal performance.

The configuration file, config.h, was successfully created.

$ make parallel
Starting installation of Amber9 (parallel) at Tue Nov 3 11:17:17 IST 2009.
cd sander; make parallel
make[1]: Entering directory `/usr/local/amber9/src/sander'
./checkparconf
cpp -traditional -P -DMPI evb_vars.f > _evb_vars.f
ifort -c -w95 -mp1 -O0 -FR -o evb_vars.o _evb_vars.f
make[1]: ifort: Command not found
make[1]: *** [evb_vars.o] Error 127
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2

On Mon, Nov 2, 2009 at 8:30 PM, Nicolas SAPAY
<nicolas.sapay_at_cermav.cnrs.fr>wrote:

>
> > Dear Nicolas,
> > My simulation is giving more or less similar time
> result.
> > With a system 15500 atoms in a single processor system of 2.66 GHz (0.8
> nm
> > with PME) in a fedora 9 OS with GNU compiler it is taking 6 hours to
> > complete 150 ps simulation. My computer has 4 processors but the job is
> > running in 1 processor only. By any means can I distribute by jobs in
> all
> > the processors.
>
> If you want to do something else that minimization, you must run your jobs
> on several procs :)
> To do that, you need a message passing interface (MPI) as well as
> recompiling Amber. Common MPIs are MPICH2 and LAMMPI. You can install them
> with a yum command. Do not install both! Install only one of them. I also
> recommend you to have a look in the Amber manual and in the mailing list
> archives. There is plenty of information about running Amber in parallel.
>
> Nicolas
>
> >
> >
> > On Mon, Nov 2, 2009 at 7:49 PM, Nicolas SAPAY
> > <nicolas.sapay_at_cermav.cnrs.fr>wrote:
> >
> >> Hello Nicholus,
> >>
> >> This is not that easy to answer to your question since the performance
> >> of
> >> your calculation depends on many factors, including:
> >> - the number of processors you are using;
> >> - their frequency;
> >> - the hardware/software used by processors to communicate;
> >> - the number of particles in your system;
> >> - whether you are using PME or not;
> >> - ...
> >>
> >> I made a test recently with a 30000 atoms system on a single Intel proc
> >> at
> >> 2.4 GHz (cutoff at 0.8 nm with PME). The OS was Fedora 10 and I used the
> >> GNU compiler. I was able to compute 0.41 ns per day which is not
> >> particularly great but sufficient to setup, minimize and equilibrate a
> >> system (in bulk water).
> >>
> >> Cheers,
> >> Nicolas
> >>
> >> > On Mon, Nov 2, 2009 at 1:01 PM, manoj singh <mks.amber_at_gmail.com>
> >> wrote:
> >> >
> >> >> You can do a quick benchmarking for your system by running few ps
> >> >> simulations. The simulation time is proportional to the length of the
> >> >> simulation.
> >> >>
> >> >> On Mon, Nov 2, 2009 at 1:08 AM, nicholus bhattacharjee <
> >> >> nicholusbhattacharjee_at_gmail.com> wrote:
> >> >>
> >> >> > Dear community,
> >> >> > I am running a protein simulation in my
> >> IBM
> >> >> 3400
> >> >> > server (specification
> >> >> > http://www-07.ibm.com/systems/in/x/hardware/tower/x3400/specs.html
> )
> >> >> with
> >> >> > AMBER 9. My protein is 50 amino acid long. I am doing an explicit
> >> >> solvent
> >> >> > simulation. Can anybody suggest what is the maximum time needed for
> >> >> this
> >> >> > simulation.
> >> >> >
> >> >> > --
> >> >> > Nicholus Bhattacharjee
> >> >> > PhD Scholar
> >> >> > Department of Chemistry
> >> >> > University of Delhi
> >> >> > Delhi-110007 (INDIA)
> >> >> > Phone: 9873098743(M)
> >> >> > _______________________________________________
> >> >> > 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
> >> >>
> >> >
> >> >
> >> > My machine is taking 1/2 hour for 10 ps simulation. Is this very long?
> >> > --
> >> > Nicholus Bhattacharjee
> >> > PhD Scholar
> >> > Department of Chemistry
> >> > University of Delhi
> >> > Delhi-110007 (INDIA)
> >> > Phone: 9873098743(M)
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER_at_ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> --
> >> [ Nicolas Sapay - Post-Doctoral Fellow ]
> >> CERMAV - www.cermav.cnrs.fr
> >> BP53, 38041 Grenoble cedex 9, France
> >> Phone: +33 (0)4 76 03 76 44/53
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> [ Nicolas Sapay - Post-Doctoral Fellow ]
> CERMAV - www.cermav.cnrs.fr
> BP53, 38041 Grenoble cedex 9, France
> Phone: +33 (0)4 76 03 76 44/53
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
_______________________________________________
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AMBER_at_ambermd.org
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