[Wien] System configuration

Thu May 23 20:37:03 CEST 2019

I did the patching but after compiling I am getting the
SRC_dstart/compile.msg:gfortran: error: buffered_io: No such file or
directory
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-mp1’
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-pad’
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_dstart/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_dstart/compile.msg:make[1]: *** [module.o] Error 1
SRC_dstart/compile.msg:make: *** [para] Error 2
SRC_hf/compile.msg:gfortran: error: buffered_io: No such file or directory
SRC_hf/compile.msg:gfortran: error: unrecognized command line option ‘-mp1’
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_hf/compile.msg:gfortran: error: unrecognized command line option ‘-pad’
SRC_hf/compile.msg:gfortran: error: unrecognized command line option ‘-ip’;
did you mean ‘-p’?
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1
SRC_hf/compile.msg:make: *** [rp] Error 2
SRC_hf/compile.msg:gfortran: error: buffered_io: No such file or directory
SRC_hf/compile.msg:gfortran: error: unrecognized command line option ‘-mp1’
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_hf/compile.msg:gfortran: error: unrecognized command line option ‘-pad’
SRC_hf/compile.msg:gfortran: error: unrecognized command line option ‘-ip’;
did you mean ‘-p’?
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_hf/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1
SRC_hf/compile.msg:make: *** [cp] Error 2
SRC_lapw1/compile.msg:gfortran: error: buffered_io: No such file or
directory
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-mp1’
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-pad’
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1
SRC_lapw1/compile.msg:make: *** [rp] Error 2
SRC_lapw1/compile.msg:gfortran: error: buffered_io: No such file or
directory
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-mp1’
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-pad’
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_lapw1/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1
SRC_lapw1/compile.msg:make: *** [cp] Error 2
SRC_lapw2/compile.msg:gfortran: error: buffered_io: No such file or
directory
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-mp1’
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-pad’
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1
SRC_lapw2/compile.msg:make: *** [rp] Error 2
SRC_lapw2/compile.msg:gfortran: error: buffered_io: No such file or
directory
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-mp1’
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-pad’
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_lapw2/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1
SRC_lapw2/compile.msg:make: *** [cp] Error 2
SRC_lapwso/compile.msg:gfortran: error: buffered_io: No such file or
directory
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-mp1’
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-pad’
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_lapwso/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_lapwso/compile.msg:make[1]: *** [reallocate.o] Error 1
SRC_lapwso/compile.msg:make: *** [para] Error 2
SRC_nmr/compile.msg:gfortran: error: buffered_io: No such file or directory
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option ‘-mp1’
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option ‘-pad’
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_nmr/compile.msg:make[1]: *** [modules.o] Error 1
SRC_nmr/compile.msg:make: *** [rp] Error 2
SRC_nmr/compile.msg:gfortran: error: buffered_io: No such file or directory
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option ‘-mp1’
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-prec_div’; did you mean ‘-mrecip’?
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-pc80’; did you mean ‘-mpc80’?
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option ‘-pad’
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-ip’; did you mean ‘-p’?
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-traceback’
SRC_nmr/compile.msg:gfortran: error: unrecognized command line option
‘-assume’; did you mean ‘-msse’?
SRC_nmr/compile.msg:make[1]: *** [modules.o] Error 1
SRC_nmr/compile.msg:make: *** [cp] Error 2

On Fri, May 24, 2019 at 12:03 AM Pavel Ondračka <pavel.ondracka at email.cz>
wrote:

> Hi Indranil,
>
> I'm sending this again this time also to the list (haven't noticed you
> removed it), in the hope it might be useful for someone optimizing with
> gfortran as well...
>
> Pavel
>
> Well,
>
> first we need to figure out why is your serial lapw so slow...
> You definitely don't have the libmvec patches, however almost two min
> runtime suggest that even your BLAS might be bad?
>
> In the test_case folder run:
> $ grep "TIME HAMILT" test_case.output1
> and post the output. Also please go to the Wien2k folder and send the
> output of
> $ cat WIEN2k_OPTION
> and
> $ ldd lapw1
>
> Next Wien2k version will have this simplified, however for now some
> patching needs to be to be done. The other option would be to get MKL
> and ifort from Intel and use it instead...
>
> Anyway if you don't want MKL, you need to download the attached patch
> to the SRC_lapw1 folder in Wien2k base folder.
> Go to the folder, and apply the patch with (you might need the patch
> package for that)
> $ patch -p1 < lapw1.patch
> then set the FOPT compile flags via siteconfig to:
> -ffree-form -O2 -ffree-line-length-none -march=native -ftree-vectorize
> -DHAVE_LIBMVEC -fopenmp
> and recompile lapw1.
> Now when you do again
> $ ldd lapw1
> it should show line with "libmvec.so.1 => /lib64/libmvec.so.1"
>
> Compare timings again with the test_case.
> Also try:
> $ OMP_NUM_THREADS=2 x lapw1
> $ OMP_NUM_THREADS=4 x lapw1
>
> And after each run show total timings as well as
> $ grep "TIME HAMILT" test_case.output1
> Hopefully, you are already linking the multithreaded Openblas (but
> dunno what is the Ubuntu default)...
>
> I'll help you with the parallel execution in the next step.
>
> Best regards
> Pavel
>
> On Thu, 2019-05-23 at 18:58 +0530, Indranil mal wrote:
> > Dear sir
> >
> > After running x lapw1 I got the following
> >
> > ~/test_case$ x lapw1
> > STOP LAPW1 END
> > 114.577u 0.247s 1:54.82 99.9% 0+0k 0+51864io 0pf+0w
> >
> > I am using parallel k point execution only 8 GB memory is in use and
> > for 100 atom (100 kpoints) calculation it is taking around 12 hours
> > to complete one cycle.
> > please help me.
> >
> > Thanking you
> >
> > Indranil
> >
> > On Thu, May 23, 2019 at 11:22 AM Pavel Ondračka <
> > pavel.ondracka at email.cz> wrote:
> > > Hi Indranil,
> > >
> > > While the k-point parallelization is usually the most efficient
> > > (provided you have sufficient number of k-points) and does not need
> > > any
> > > extra libraries, for 100atoms case it might be problematic to fit
> > > 12
> > > processes into 32GB of memory. I assume you are already using it
> > > since
> > > you claim to run on two cores?
> > >
> > > Instead check what is the maximum memory requirement of lapw1 when
> > > run
> > > in serial and based on that find how much processes you can run in
> > > parallel, than for each place one line "1:localhost" into .machines
> > > file (there is no need to copy .machines from templates, or use
> > > random
> > > scripts, instead read the userguide to understand what you are
> > > doing,
> > > it will save you time in the long run). If you can run at least few
> > > k-
> > > points in parallel it might be enough to speed it up significantly.
> > >
> > > For MPI you would need openmpi-devel scalapack-devel and fftw3-
> > > devel
> > > (I'm not sure how exactly are they named on Ubuntu) packages.
> > > Especially the scalapack configuration could be tricky, it is
> > > probably
> > > easiest to start with lapw0 as this needs only MPI and fftw.
> > >
> > > Also based on my experience with default gfortran settings, it is
> > > likely that you don't have even optimized the single core
> > > performance,
> > > try to download the serial benchmark
> > > http://susi.theochem.tuwien.ac.at/reg_user/benchmark/test_case.tar.gz
> > > untar, run x lapw1 and report timings (on average i7 CPU it should
> > > take
> > > below 30 seconds, if it takes significantly more, you will need
> > > some
> > > more tweaks).
> > >
> > > Best regards
> > > Pavel
> > >
> > > On Thu, 2019-05-23 at 10:42 +0530, Dr. K. C. Bhamu wrote:
> > > > Hii,
> > > >
> > > > If you are doing k-point parallel calculation (having number of
> > > k-
> > > > points in IBZ more then 12) then use below script on terminal
> > > where
> > > > you want to run the calculation or use in your job script with
> > > -p
> > > > option in run(sp)_lapw (-so).
> > > >
> > > > if anyone knows how to repeat a nth line m times in a file then
> > > this
> > > > script can be changed.
> > > >
> > > > Below script simply coping machine file from temple directory and
> > > > updating it as per your need.
> > > > So you do not need copy it, open it in your favorite editor and
> > > do it
> > > > manually.
> > > >
> > > > cp $WIENROOT/SRC_templates/.machines . ; grep localhost .machines
> > > |
> > > > perl -ne 'print $_ x 6' > LOCALHOST.dat ; tail -n 2 .machines >
> > > > grang.dat ; sed '22,25d' .machines > MACHINE.dat ; cat
> > > MACHINE.dat
> > > > localhost.dat grang.dat > .machines ; rm LOCALHOST.dat
> > > MACHINE.dat
> > > > grang.dat
> > > >
> > > > regards
> > > > Bhamu
> > > >
> > > >
> > > > On Wed, May 22, 2019 at 10:52 PM Indranil mal <
> > > indranil.mal at gmail.com
> > > > > wrote:
> > > > > respected sir/ Users,
> > > > > I am using a PC with intel i7 8th gen (with
> > > 12
> > > > > cores) 32GB RAM and 2TB HDD with UBUNTU 18.04 LTS. I have
> > > installed
> > > > > OpenBLAS-0.2.20 and using GNU FORTRAN and c compiler. I am
> > > trying
> > > > > to run a system with 100 atoms only two cores are using the
> > > rest of
> > > > > them are idle and the calculation taking a too long time. I
> > > have
> > > > > not installed mpi ScaLAPACK or elpa. Please help me what should
> > > I
> > > > > do to utilize all of the cores of my cpu.
> > > > >
> > > > >
> > > > >
> > > > > Thanking you
> > > > >
> > > > > Indranil
> > > > > _______________________________________________
> > > > > Wien mailing list
> > > > > Wien at zeus.theochem.tuwien.ac.at
> > > > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > > > > SEARCH the MAILING-LIST at:
> > > > >
> > > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> > > >
> > > > _______________________________________________
> > > > Wien mailing list
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> > >
> > > _______________________________________________
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