Hi,
MMPBSA.py.MPI is built when you build AmberTools 1.5 in parallel, not Amber
11. Thus, running "make parallel" in $AMBERHOME/AmberTools/src after
running ./configure -mpi gnu is what you need to do. (You could also go to
the $AMBERHOME/AmberTools/src/mmpbsa_py directory and run the "make
parallel" command -- it should build it for you).
About the errors you're seeing -- this is a sign that your environment
variables or something may be out of whack. I suggest trying to recompile
AmberTools 1.5 in serial, then in parallel.
HTH,
Jason
2011/9/29 Marek Maly <marek.maly.ujep.cz>
> Hi Jason,
> thanks for a prompt reply !
>
> Regarding #1 I tried your suggestion and it works perfectly !
>
> Regarding #2 I didn't find MMPBSA.MPI in $AMBERHOME/bin nor
>
> MMPBSA.py.MPI which I suppose to be located in
> $AMBERHOME/AmberTools/src/mmpbsa_py
> where I found MMPBSA.py script. Then I found in Amber11 manual :
>
>
> -------------------------------------------------------------------------------------
> 10.3.3.2 Parallel (MPI) version
> This version is installed with Amber during the parallel install. The
> python package mpi4py is included with the MMPBSA.py source code and must
> be successfully installed in order to run the MPI version of MMPBSA ......
>
>
> --------------------------------------------------------------------------------------
>
> So I successfully installed also parallel version (./configure -mpi gnu)
> of Amber11 ( having before just serial one in combination with
> AmberTools1.5 just for analyses of MD trajectories calculated with
> pmemd.CUDA on separate CUDA WorkStations. ), but unfortunately situation
> didn.t change i.e. no MMPBSA.MPI appeared in $AMBERHOME/bin. So I went to
> $AMBERHOME/AmberTools/src/mmpbsa_py and tried "make install"
> after this I have obtained plethora of errors please see below. I would be
> really grateful for any helpful suggestion ! Anyway that "forking"
> parallel approach from mm_pbsa.pl might be fully sufficient and useful
> alternative for those who don.t care about parallel Amber11
> installation or even don.t care about MPI on their machine or they have
> simply problem to install these things.
> For those might be parallelization of MMPBSA jobs although limited to
> given node sufficient solution.
> But there are for sure much more important development tasks in the queue
> I guess :))
>
> Thanks in advance for your help !
>
>
> Best wishes,
>
> Marek
>
>
> mmaly.node25 ~/_applications/amber11_node25/AmberTools/src/mmpbsa_py $
> make install
> make: Warning: File `../config.h' has modification time 8.3e+03 s in the
> future
> /bin/bash setup.sh
> Using AmberTools' python
> /home/mmaly/_applications/amber11_node25/bin/nab -o mmpbsa_py_nabnmode
> mmpbsa_entropy.nab
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In function
> `dsaupd_':
> dsaupd.f:(.text+0x11d): undefined reference to `_gfortran_compare_string'
> dsaupd.f:(.text+0x5f9): undefined reference to `_gfortran_st_write'
> dsaupd.f:(.text+0x601): undefined reference to `_gfortran_st_write_done'
> dsaupd.f:(.text+0x64d): undefined reference to `_gfortran_st_write'
> dsaupd.f:(.text+0x65f): undefined reference to `_gfortran_transfer_integer'
> dsaupd.f:(.text+0x671): undefined reference to `_gfortran_transfer_integer'
> dsaupd.f:(.text+0x683): undefined reference to `_gfortran_transfer_integer'
> dsaupd.f:(.text+0x695): undefined reference to `_gfortran_transfer_integer'
> dsaupd.f:(.text+0x6a7): undefined reference to `_gfortran_transfer_integer'
>
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x6b9):
> more undefined references to `_gfortran_transfer_integer' follow
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In function
> `dsaupd_':
> dsaupd.f:(.text+0x6cb): undefined reference to `_gfortran_transfer_real'
> dsaupd.f:(.text+0x6dd): undefined reference to `_gfortran_transfer_real'
> dsaupd.f:(.text+0x6ef): undefined reference to `_gfortran_transfer_real'
> dsaupd.f:(.text+0x701): undefined reference to `_gfortran_transfer_real'
> dsaupd.f:(.text+0x713): undefined reference to `_gfortran_transfer_real'
>
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x725):
> more undefined references to `_gfortran_transfer_real' follow
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In function
> `dsaupd_':
> dsaupd.f:(.text+0x787): undefined reference to `_gfortran_st_write_done'
> dsaupd.f:(.text+0x7a3): undefined reference to `_gfortran_compare_string'
> dsaupd.f:(.text+0x7c2): undefined reference to `_gfortran_compare_string'
> dsaupd.f:(.text+0x7e1): undefined reference to `_gfortran_compare_string'
> dsaupd.f:(.text+0x800): undefined reference to `_gfortran_compare_string'
> dsaupd.f:(.text+0x857): undefined reference to `_gfortran_compare_string'
>
> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o):dseupd.f:(.text+0x110):
> more undefined references to `_gfortran_compare_string' follow
> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o): In function
> `dseupd_':
> dseupd.f:(.text+0xb6d): undefined reference to `_gfortran_copy_string'
> dseupd.f:(.text+0xb8e): undefined reference to `_gfortran_copy_string'
> dseupd.f:(.text+0xc38): undefined reference to `_gfortran_copy_string'
> dseupd.f:(.text+0xc59): undefined reference to `_gfortran_copy_string'
> dseupd.f:(.text+0xcc2): undefined reference to `_gfortran_compare_string'
> dseupd.f:(.text+0xd60): undefined reference to `_gfortran_compare_string'
> dseupd.f:(.text+0xe23): undefined reference to `_gfortran_compare_string'
> dseupd.f:(.text+0xf6d): undefined reference to `_gfortran_compare_string'
> dseupd.f:(.text+0xf91): undefined reference to `_gfortran_compare_string'
>
> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o):dseupd.f:(.text+0xfb5):
> more undefined references to `_gfortran_compare_string' follow
> /home/mmaly/_applications/amber11/lib/arpack.a(ivout.o): In function
> `ivout_':
> ivout.f:(.text+0xb7): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0xc6): undefined reference to `_gfortran_transfer_character'
> ivout.f:(.text+0xd3): undefined reference to `_gfortran_transfer_character'
> ivout.f:(.text+0xdb): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x134): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x19b): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x1b0): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x1c5): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x1f7): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x239): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x241): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x2aa): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x311): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x326): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x33b): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x373): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x3ca): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x431): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x446): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x45b): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x48d): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x4d8): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x53f): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x554): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x569): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x59b): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x5da): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x641): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x656): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x66b): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x69d): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x6e4): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x74b): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x760): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x775): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x7a7): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x7ee): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x855): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x86a): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x87f): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x8b1): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x8ed): undefined reference to `_gfortran_st_write_done'
> ivout.f:(.text+0x954): undefined reference to `_gfortran_st_write'
> ivout.f:(.text+0x969): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x97e): undefined reference to `_gfortran_transfer_integer'
> ivout.f:(.text+0x9b0): undefined reference to `_gfortran_transfer_integer'
> /home/mmaly/_applications/amber11/lib/arpack.a(dvout.o): In function
> `dvout_':
> dvout.f:(.text+0xb7): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0xc6): undefined reference to `_gfortran_transfer_character'
> dvout.f:(.text+0xd3): undefined reference to `_gfortran_transfer_character'
> dvout.f:(.text+0xdb): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x134): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x19b): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x1b0): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x1c5): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x1f7): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x239): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x241): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x298): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x2ff): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x314): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x329): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x35b): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x3a1): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x408): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x41d): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x432): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x464): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x4a9): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x510): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x525): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x53a): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x56c): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x5aa): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x611): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x626): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x63b): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x66d): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x6aa): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x711): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x726): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x73b): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x76d): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x7b5): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x81c): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x831): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x846): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x878): undefined reference to `_gfortran_transfer_real'
> dvout.f:(.text+0x8a6): undefined reference to `_gfortran_st_write_done'
> dvout.f:(.text+0x90c): undefined reference to `_gfortran_st_write'
> dvout.f:(.text+0x921): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x936): undefined reference to `_gfortran_transfer_integer'
> dvout.f:(.text+0x968): undefined reference to `_gfortran_transfer_real'
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaup2.o): In function
> `dsaup2_':
> dsaup2.f:(.text+0xb4d): undefined reference to `_gfortran_compare_string'
> dsaup2.f:(.text+0xb71): undefined reference to `_gfortran_copy_string'
> dsaup2.f:(.text+0xcde): undefined reference to `_gfortran_copy_string'
> dsaup2.f:(.text+0xd77): undefined reference to `_gfortran_compare_string'
> dsaup2.f:(.text+0xd9b): undefined reference to `_gfortran_copy_string'
> dsaup2.f:(.text+0xef8): undefined reference to `_gfortran_compare_string'
> dsaup2.f:(.text+0xf19): undefined reference to `_gfortran_compare_string'
> dsaup2.f:(.text+0xf3a): undefined reference to `_gfortran_compare_string'
> dsaup2.f:(.text+0xf5b): undefined reference to `_gfortran_compare_string'
> dsaup2.f:(.text+0x104a): undefined reference to `_gfortran_copy_string'
> dsaup2.f:(.text+0x106b): undefined reference to `_gfortran_copy_string'
> dsaup2.f:(.text+0x108c): undefined reference to `_gfortran_copy_string'
> dsaup2.f:(.text+0x10ad): undefined reference to `_gfortran_copy_string'
> /home/mmaly/_applications/amber11/lib/arpack.a(dsesrt.o): In function
> `dsesrt_':
> dsesrt.f:(.text+0x55): undefined reference to `_gfortran_compare_string'
> dsesrt.f:(.text+0x18c): undefined reference to `_gfortran_compare_string'
> dsesrt.f:(.text+0x2e0): undefined reference to `_gfortran_compare_string'
> dsesrt.f:(.text+0x3fe): undefined reference to `_gfortran_compare_string'
> /home/mmaly/_applications/amber11/lib/arpack.a(dsgets.o): In function
> `dsgets_':
> dsgets.f:(.text+0x5d): undefined reference to `_gfortran_compare_string'
> cc failed!
> make: *** [install] Error 1
>
>
>
>
>
>
> Dne Fri, 30 Sep 2011 00:12:20 +0200 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> > Hello,
> >
> > On Thu, Sep 29, 2011 at 5:32 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> >
> >> Dear all,
> >> I just started today with MMPBSA.py (until now I used mm_pbsa.pl).
> >>
> >> After the relevant tutorial and brief reading of MMPBSA.py manual I have
> >> these two questions.
> >>
> >> #1
> >>
> >> How to proceed with MMPBSA.py if I want to calculate just (absolute)
> >> free
> >> energy of the given molecule
> >> (not dG of binding between receptor and ligand molecules).
> >>
> >
> > Just supply a complex prmtop file. If you don't provide a receptor or
> > ligand topology file, you will get this same behavior.
> >
> >
> >>
> >>
> >> In case of mm_pbsa.pl one could set just COMPLEX, RECEPTOR, LIGAND
> flags
> >> in input file like this:
> >>
> >>
> >>
> >> COMPLEX 0
> >> RECEPTOR 1
> >> LIGAND 0
> >>
> >>
> >> and mm_pbsa.pl will consider here the stand-alone molecule provided as
> >> the "formal receptor" without any complains
> >> that complex or ligand are not specified and calculate just H or S of
> >> that
> >> molecule. Is there any way how to
> >> tell MMPBSA.py that I want just calculate H, S or whole G for the given
> >> molecule ?
> >>
> >>
> >>
> >> #2
> >>
> >> In mm_pbsa.pl there is available flag PARALLEL which is very useful as
> >> it
> >> allows to define howmany frames
> >> from the given trajectory will be processed simultaneously. So for
> >> example
> >> if one has node
> >> with 8 CPU cores, setting:
> >>
> >> PARALLEL 8
> >>
> >> allow to process 8 MD frames simultaneously (probably without need of
> >> MPI
> >> ?).
> >>
> >
> > Yes. The way mm_pbsa.pl works is by forking off processes. This limits
> > parallel performance to a single node, though, since the simple forker
> > doesn't know enough to launch processes on remote nodes. MPI, on the
> > other
> > hand, is built for normal, parallel Amber simulations and is easily run
> > on
> > distributed systems (across multiple nodes). Since there were good
> > python
> > bindings for MPI, we decided to use MPI to parallelize MMPBSA.py.
> >
> >
> >> In case of python version just usage of MMPBSA.py.MPI instead MMPBSA.py
> >> brings the similar
> >> possibility am I right ?
> >>
> >
> > Correct. mpi4py is built automatically with AmberTools 1.5. I would
> > suggest using AmberTools 1.5 version, in which case you have to use
> > MMPBSA
> > and MMPBSA.MPI, which are shell scripts that invoke MMPBSA.py and
> > MMPBSA.py.MPI with the appropriate variables.
> >
> > HTH,
> > Jason
> >
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
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Received on Thu Sep 29 2011 - 22:30:02 PDT
