Hi Jason,
Thanks a lot ! The problem is solved and MMPBSA.MPI works perfectly !
I would like to ask you about "saltcon" GB parameter. I am doing
simulations under
0.15 M of NaCl. Is it in your opinion this concentration still acceptable
for GB,
or is better to go on 0.1 to be still in safe range regarding
assumptions/approximations
in GB theory ?
I am also curious why usage of sander ( use_sander=1 ) causes so
significant slowdown comparing
to case when mmpbsa_py_energy is used ( use_sander=0 ) .
Thanks once again !
Best wishes,
Marek
Dne Fri, 30 Sep 2011 07:10:47 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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
>>
>
>
>
--
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
Received on Fri Sep 30 2011 - 10:00:03 PDT
