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.ondra...@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.ondra...@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....@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@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 > > > > Wien@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 > > > Wien@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 > Wien@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 >
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