Hello,
nicholus bhattacharjee a écrit :
> 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.
I'm not an Amber wizard, just a humble user. I'm absolutely not aware of
the different kind of licences provided by the Amber developers. To
check if you are really running on several procs or not, you can do a
quick benchmark of your system by running few ns on 1, 2, 3, ... procs
and see if the perfs are improved.
> 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
IIRC MKL_HOME is a variable present when the Inter compiler is installed
on a machine. Is it the case here?
> .
>
> 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
>
This error clearly says that the compiler you're using is not in your
path. Is the Intel Fortran compiler installed on your machine? If yes,
it is probably not in the default path
> 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.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.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.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.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.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.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.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.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.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.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
>
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Received on Tue Nov 03 2009 - 01:00:02 PST
