[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
Long Zhang
lzhang6789 at gmail.com
Fri Feb 22 21:13:02 CET 2013
Thank you. I found related contents in sec 5.5.5. I understand it now.
On Fri, Feb 22, 2013 at 3:05 PM, Peter Blaha
<pblaha at theochem.tuwien.ac.at>wrote:
> No. Please read the UG about parallelization. k-point parallelization is
> done via scripts.
>
> Am 22.02.2013 20:28, schrieb Long Zhang:
>
>> Thank you for the information.
>> I think I had wrong idea about k-point parallel. If it doesn't use
>> OpenMP then it's perfectly fine for me. I'll drop the idea of
>> finegrained parallel in this installation.
>>
>> Just want to confirm, for using k-point parallel only, MPICH2 is still
>> required, is that right?
>>
>> Thanks.
>> Long
>>
>>
>>
>>
>> On Fri, Feb 22, 2013 at 11:04 AM, Laurence Marks
>> <L-marks at northwestern.edu <mailto:L-marks at northwestern.**edu<L-marks at northwestern.edu>>>
>> wrote:
>>
>> As Peter said, the simplest approach is just k-point parallel which
>> does not need OpenMP. The rate limiting steps are lapack calls which
>> the Intel mkl is good for.
>>
>> Whether mpi is good for a small cluster such as you have in not so
>> clear. Peter has benchmarked the mpi version and his conclusion is
>> that it is not useful; I have benchmarked on my cluster and I have
>> consistently found the mpi versions to be faster than the Intel
>> threading. I suspect that it really depends upon many details specific
>> to the systems, for instance cross-core optimizations, network and
>> memory speed....
>>
>> Not a complete answer, but for certain the simplest approach is to
>> just use k-point parallel.
>>
>> On Fri, Feb 22, 2013 at 9:55 AM, Long Zhang <lzhang6789 at gmail.com
>> <mailto:lzhang6789 at gmail.com>> wrote:
>> >
>> > That's true I agree. If the k-point parallel version does not
>> need mpi, then
>> > it's OpenMP I suppose (please correct me if it's not). But I
>> really don't
>> > want to run OpenMP because it will mess my other applications up.
>> >
>> > I am building it on a small server of 2 Opteron 12-core cpus.
>> It's just a
>> > dual-cpu system, not a cluster. I am not sure if I can gain
>> enough speed-up
>> > by using 24 cores. Anyway if I want a little k-point parallel,
>> can I choice
>> > to use mpi? or there is no such choice at all?
>> >
>> > Thank you very much.
>> > Long
>> >
>> >
>> > On Fri, Feb 22, 2013 at 3:07 AM, Peter Blaha
>> <pblaha at theochem.tuwien.ac.at <mailto:pblaha at theochem.**tuwien.ac.at<pblaha at theochem.tuwien.ac.at>
>> >>
>>
>> > wrote:
>> >>
>> >> I keep saying this all the time:
>> >>
>> >> The mpi-parallel version needs special hardware !
>> >>
>> >> It is not of much use on a single quadcore-cpu.
>> >> A cluster needs a fast network like infiniband.
>> >>
>> >> Only then the installation of the mpi-version make sense.
>> >>
>> >> We have a k-point parallel version, which does not need mpi, but
>> is
>> >> perfect for a small cluster with a common NFS filesystem.
>> >>
>> >>
>> >> Am 22.02.2013 06:20, schrieb Long Zhang:
>> >>>
>> >>>
>> >>> Hello,
>> >>>
>> >>> I am trying to install the current version 12.1 on Ubuntu 12.04
>> >>> (64-bit). I met some problem related to mpi, can someone please
>> give me
>> >>> some hint? Thanks in advance.
>> >>>
>> >>> The situation is like this, on a freshly installed Ubuntu 12.04
>> 64bit, I
>> >>> installed current version Intel Fortran Composer XE 2013.2.146,
>> and
>> >>> installed MPICH2 and FFTW3 via Ubuntu Software Center.
>> >>>
>> >>> Before run the siteconfig_lapw, I checked
>> >>> which ifort
>> >>> /opt/intel/composer_xe_2013.2.**146/bin/intel64/ifort
>> >>> which mpif90
>> >>> /usr/bin/mpif90
>> >>>
>> >>> and did the following 3 lines in the terminal
>> >>> source /opt/intel/composer_xe_2013.2.**146/bin/compilervars.sh
>> intel64
>> >>> export
>> >>>
>> >>>
>> LD_LIBRARY_PATH=$LD_LIBRARY_**PATH:/opt/intel/composer_xe_**
>> 2013.2.146/mkl/lib/intel64
>> >>> export MKLROOT=/opt/intel/composer_**xe_2013.2.146/mkl/
>> >>>
>> >>> Then I run the siteconfig_lapw, and selected system as
>> "ifort12+mkl"
>> >>> (the first one), selected compilers as "ifort" and "cc", selected
>> >>> "finegrained parallel" and "mpif90", and got error message like
>> this:
>> >>>
>> >>> ------------------------------**----------------- cut1
>> >>> ------------------------------**-----------------
>> >>> Compile time errors (if any) were:
>> >>> SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_hf/compile.msg:make: *** [rp] Error 2
>> >>> SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_hf/compile.msg:make: *** [cp] Error 2
>> >>> SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_lapw0/compile.msg:make: *** [para] Error 2
>> >>> SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_lapw1/compile.msg:make: *** [rp] Error 2
>> >>> SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_lapw1/compile.msg:make: *** [cp] Error 2
>> >>> SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_lapw2/compile.msg:make: *** [rp] Error 2
>> >>> SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1
>> >>> SRC_lapw2/compile.msg:make: *** [cp] Error 2
>> >>> ------------------------------**----------------- cut1
>> >>> ------------------------------**-----------------
>> >>>
>> >>> I looked into SRC_lapw1/compile.msg, and the detailed error is:
>> >>>
>> >>> ------------------------------**----------------- cut2
>> >>> ------------------------------**-----------------
>> >>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3
>> >>> -traceback -DParallel -c modules_tmp_.F
>> >>>
>> >>>
>> ------------------------------**------------------------------**
>> --------------
>> >>> The Open MPI wrapper compiler was unable to find the specified
>> compiler
>> >>> gfortran in your PATH.
>> >>>
>> >>> Note that this compiler was either specified at configure time
>> or in
>> >>> one of several possible environment variables.
>> >>>
>> >>>
>> ------------------------------**------------------------------**
>> --------------
>> >>> make[1]: *** [modules.o] Error 1
>> >>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_**lapw1'
>> >>> make: *** [rp] Error 2
>> >>> ------------------------------**----------------- cut2
>> >>> ------------------------------**-----------------
>> >>>
>> >>> It seems OpenMPI was invoked and it looked for gfortran. I
>> don't have
>> >>> gfortran installed at all, but I found I have openmpi
>> installed. I then
>> >>> used Ubuntu Software Center to search openmpi and uninstalled
>> related
>> >>> packages. I restarted the system and repeated the
>> siteconfig_lapw.
>> >>> However I still get error message, not same but similar, it
>> still looks
>> >>> for gfortran, for examplethe SRC_lapw1/compile.msg shows:
>> >>>
>> >>>
>> >>> ------------------------------**----------------- cut3
>> >>> ------------------------------**-----------------
>> >>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3
>> >>> -traceback -DParallel -c modules_tmp_.F
>> >>> /usr/bin/mpif90: line 370: gfortran: command not found
>> >>> make[1]: *** [modules.o] Error 127
>> >>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_**lapw1'
>> >>> make: *** [rp] Error 2
>> >>> ------------------------------**----------------- cut3
>> >>> ------------------------------**-----------------
>> >>>
>> >>> I did not specify to use gfortran anywhere in the setupof
>> >>> siteconfig_lapw, I don't see why mpif90 keeps looking for it.
>> How can I
>> >>> fix this problem? Thanks a lot.
>> >>>
>> >>> Regards,
>> >>> Long Zhang
>> >>>
>> >>>
>> >>> ______________________________**_________________
>> >>> Wien mailing list
>> >>> Wien at zeus.theochem.tuwien.ac.**at<Wien at zeus.theochem.tuwien.ac.at>
>> <mailto:Wien at zeus.theochem.**tuwien.ac.at<Wien at zeus.theochem.tuwien.ac.at>
>> >
>>
>> >>> http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wien<http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien>
>> >>>
>> >>
>> >> --
>> >> Peter Blaha
>> >> Inst.Materials Chemistry
>> >> TU Vienna
>> >> Getreidemarkt 9
>> >> A-1060 Vienna
>> >> Austria
>> >> +43-1-5880115671 <tel:%2B43-1-5880115671>
>>
>> >>
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>> >
>>
>> >> http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wien<http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien>
>> >
>> >
>>
>>
>>
>> --
>> Professor Laurence Marks
>> Department of Materials Science and Engineering
>> Northwestern University
>> www.numis.northwestern.edu <http://www.numis.**northwestern.edu<http://www.numis.northwestern.edu>
>> >
>> 1-847-491-3996 <tel:1-847-491-3996>
>>
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought"
>> Albert Szent-Gyorgi
>> ______________________________**_________________
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>> Wien at zeus.theochem.**tuwien.ac.at <Wien at zeus.theochem.tuwien.ac.at>>
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>>
>>
>>
>>
>>
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>>
> --
> Peter Blaha
> Inst.Materials Chemistry
> TU Vienna
> Getreidemarkt 9
> A-1060 Vienna
> Austria
> +43-1-5880115671
> ______________________________**_________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.**at <Wien at zeus.theochem.tuwien.ac.at>
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