[Wien] Problems with mpi for Wien12.1
N.b., I meant lapw0 everywhere as I believe you said that is where the problem is. If it is in lapw1, then change everything to lapw1 in my email. --- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi On Aug 28, 2012 10:34 PM, "Laurence Marks" wrote: > Hmmm. I was hoping for something human readable like a traceback showing > where it died. Please check both the lapw0.error files and case.dayfile to > see if they gave anything useful. Also, what are the last few lines of > case.output? > > You may get somewhere by running the mpirun command by hand, I have seen > this help. If you understand csh then you want to add an echo $tt at the > relevant location in lapw0para. > > If not you can change the first line of lapw1para to "-xf" rather than > just "-f". Then do x lapw0 -p again. You will get a hundred or so lines of > output one of which towards the end will be something like > > "mpirun -np 12 ..." > > Then paste this line by itself in a terminal. Maybe then something human > readable will emerge. > > Unfortunately debugging mpi is not trivial, and a SIGSEV can also be non > trivial as the error may not appear at the right place, making life more > fun. > > Do you gave totalview or a similar mpi debugger available? You can get a > demo version of totalview free for I believe 30 days. > > --- > Professor Laurence Marks > Department of Materials Science and Engineering > Northwestern University > www.numis.northwestern.edu 1-847-491-3996 > "Research is to see what everybody else has seen, and to think what nobody > else has thought" > Albert Szent-Gyorgi > On Aug 28, 2012 10:09 PM, "Paul Fons" wrote: > >> I compiled fftw3 using the Intel suite as well. The appropriate line >> from config.log reads >> >> ./configure CC=icc F77=ifort MPICC=mpiicc --prefix=/opt/local >> --enable-mpi --enable-threads --prefix=/opt/local/fftw3 >> >> I note that the configuration file only calls for a mpicc compiler (and >> I used the Intel compiler) and not a fortran compiler. The compiled code >> (mpi-bench does work fine with the Intel mpirun). >> >> >> After commenting out the call W2kinit subroutine and recompiling lapw0 >> (via the siteconfig script), I attempted to run run_lapw in both serial and >> parallel forms as you can see below. The serial form worked fine >> >> Paul >> >> matstud at ursa:~/WienDisk/Fons/GaAs> run_lapw >> LAPW0 END >> LAPW1 END >> LAPW2 END >> CORE END >> MIXER END >> ec cc and fc_conv 1 1 1 >> >> > stop >> >> >> matstud at ursa:~/WienDisk/Fons/GaAs> run_lapw -p >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> forrtl: severe (174): SIGSEGV, segmentation fault occurred >> >> > stop error >> >> >> >> On Aug 28, 2012, at 9:16 AM, Laurence Marks wrote: >> >> One suggestion: comment out the line towards the top of lapw0.F >> >> call W2kinit >> >> You should get a more human readable error message. >> >> As an addendum, was fftw3 compiled with mpiifort? I assume from your >> email that it was, just checking. >> >> N.B., there is a small chance that this will hang your computer. >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> >> >> Dr. Paul Fons >> Senior Research Scientist >> Functional Nano-phase-change Research Team >> Nanoelectronics Research Institute >> National Institute for Advanced Industrial Science & Technology >> METI >> >> AIST Central 4, Higashi 1-1-1 >> Tsukuba, Ibaraki JAPAN 305-8568 >> >> tel. +81-298-61-5636 >> fax. +81-298-61-2939 >> >> email: *paul-fons at aist.go.jp* >> >> The following lines are in a Japanese font >> >> ?305-8562 ? 1-1-1 >> ? >> ?? >> >> ? >> >> >> >> >> >> >> -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120828/5c5ca9e3/attachment.htm>
[Wien] Problems with mpi for Wien12.1
Hmmm. I was hoping for something human readable like a traceback showing where it died. Please check both the lapw0.error files and case.dayfile to see if they gave anything useful. Also, what are the last few lines of case.output? You may get somewhere by running the mpirun command by hand, I have seen this help. If you understand csh then you want to add an echo $tt at the relevant location in lapw0para. If not you can change the first line of lapw1para to "-xf" rather than just "-f". Then do x lapw0 -p again. You will get a hundred or so lines of output one of which towards the end will be something like "mpirun -np 12 ..." Then paste this line by itself in a terminal. Maybe then something human readable will emerge. Unfortunately debugging mpi is not trivial, and a SIGSEV can also be non trivial as the error may not appear at the right place, making life more fun. Do you gave totalview or a similar mpi debugger available? You can get a demo version of totalview free for I believe 30 days. --- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi On Aug 28, 2012 10:09 PM, "Paul Fons" wrote: > I compiled fftw3 using the Intel suite as well. The appropriate line > from config.log reads > > ./configure CC=icc F77=ifort MPICC=mpiicc --prefix=/opt/local --enable-mpi > --enable-threads --prefix=/opt/local/fftw3 > > I note that the configuration file only calls for a mpicc compiler (and > I used the Intel compiler) and not a fortran compiler. The compiled code > (mpi-bench does work fine with the Intel mpirun). > > > After commenting out the call W2kinit subroutine and recompiling lapw0 > (via the siteconfig script), I attempted to run run_lapw in both serial and > parallel forms as you can see below. The serial form worked fine > > Paul > > matstud at ursa:~/WienDisk/Fons/GaAs> run_lapw > LAPW0 END > LAPW1 END > LAPW2 END > CORE END > MIXER END > ec cc and fc_conv 1 1 1 > > > stop > > > matstud at ursa:~/WienDisk/Fons/GaAs> run_lapw -p > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > forrtl: severe (174): SIGSEGV, segmentation fault occurred > > > stop error > > > > On Aug 28, 2012, at 9:16 AM, Laurence Marks wrote: > > One suggestion: comment out the line towards the top of lapw0.F > > call W2kinit > > You should get a more human readable error message. > > As an addendum, was fftw3 compiled with mpiifort? I assume from your email > that it was, just checking. > > N.B., there is a small chance that this will hang your computer. > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > > Dr. Paul Fons > Senior Research Scientist > Functional Nano-phase-change Research Team > Nanoelectronics Research Institute > National Institute for Advanced Industrial Science & Technology > METI > > AIST Central 4, Higashi 1-1-1 > Tsukuba, Ibaraki JAPAN 305-8568 > > tel. +81-298-61-5636 > fax. +81-298-61-2939 > > email: *paul-fons at aist.go.jp* > > The following lines are in a Japanese font > > ?305-8562 ? 1-1-1 > ? > ?? > > ? > > > > > > > -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120828/078e27b3/attachment.htm>
[Wien] Fwd: problem with display of SCF results with Wi2ek version 8
Thank you prof. could you let me know the solution to this problem? i have checked mailing list but unfortunately i can not solve it. On 8/27/12, Peter Blaha wrote: > Some graphics options of old versions of WIEN2k are not compatible with new > gnuplot versions. > > There were several posts on the mailing list describing these problems. > > Am 27.08.2012 06:03, schrieb Muhammad Sajjad: >> Respected Group Members >> I am running wien version 8 on a machine of type Dell Core I5 Desktop >> with operating system FEDORA17 (64 BIT) , fortran compiler >> "intel_fortran_composer_xe_2011_lin". The purpose of my calculations >> is to get quantity ELECTRON DENSITY (ED) and DOS. I have completed SCF >> but when i try to get ED & DOS then the plots do not appear.what does >> happen there, i have attached it herewith the mail. please see the >> attachment. even though i have installed gnuplot with command yum >> install gnuplot. >> Also when i run SCF with 11 version then it works but i want to use 8 >> version as i have some problems with version 11. Please help me in >> this regard. In advance, thanks a lot. >> >> Kind Regards >> M. Sajjad >> >> >> >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> > > -- > - > Peter Blaha > Inst. Materials Chemistry, TU Vienna > Getreidemarkt 9, A-1060 Vienna, Austria > Tel: +43-1-5880115671 > Fax: +43-1-5880115698 > email: pblaha at theochem.tuwien.ac.at > - > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >
[Wien] Thin film calculations using wien2k Reg.
You may have a look at some lecture notes at www.wien2k.at (mainly Blaha_WIEN2k-getting_started.pdf) Am 27.08.2012 15:03, schrieb yedu kondalu: > Dear all, > > So far, we are dealing with bulk material (crystalline solids) properties > such as electronic structure and optical properties using wien2k. > Now, we are trying to calculate same properties for thin films. As a first > step, we need to generate case.struct for the thin film. > > For this, we have searched in wien2k forum to do these kind of calculations, > we didn't find any tutorial type input for thin film structure file. > As a beginners, We need some basic guidelines to build the thin film > structure file. So, We are requesting some one to provide the preliminary > > details to do so. What are all the changes in structure file from bulk to > thin films ???/ > / > Thanks in advance > > Regards > KONDAL > > > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] Problems with mpi for Wien12.1
Dear Prof. Blaha, I was under the impression that I had replied promptly to your initial question. I apologize for the delay. I have been using the mpi complier of the intel mpi (4.0.3) suite, namely mpiifort. Here are the results of the which operation and the underlying version of the fortran compiler. Thank you for your hep. matstud at ursa:~/Wien2K> which mpiifort /opt/intel/impi/4.0.3.008/intel64/bin/mpiifort matstud at ursa:~/Wien2K> mpiifort --version ifort (IFORT) 12.1.5 20120612 Copyright (C) 1985-2012 Intel Corporation. All rights reserved. Below find a short sequence from a recompile of lapw1 using siteconfig. I note that mpiifort is being used. touch .parallel make PARALLEL='-DParallel' TYPE='REAL' TYPE_COMMENT='\!_REAL' \ ./lapw1_mpi FORT=mpiifort FFLAGS=' -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback '-DParallel'' make[1]: Entering directory `/home/matstud/Wien2K_12_1/SRC_lapw1' modules.F: REAL version extracted mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c modules_tmp_.F mv modules_tmp_.o modules.o rm modules_tmp_.F mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c abc.f atpar.F: REAL version extracted mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c atpar_tmp_.F mv atpar_tmp_.o atpar.o rm atpar_tmp_.F calkpt.F: REAL version extracted mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c calkpt_tmp_.F mv calkpt_tmp_.o calkpt.o rm calkpt_tmp_.F mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c cbcomb.f mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c coors.f dscgst.F: REAL version extracted mpiifort -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include/intel64/lp64 -I/opt/intel/composer_xe_2011_sp1.11.339/mkl/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback -DParallel -c dscgst_tmp_.F mv dscgst_tmp_.o dscgst.o rm dscgst_tmp_.F and the final linking step mv W2kinit_tmp_.o W2kinit.o rm W2kinit_tmp_.F mpiifort -o ./lapw1c_mpi abc.o atpar.o bandv1.o calkpt.o cbcomb.o coors.o cputim.o dblr2k.o dgeqrl.o dgewy.o dgewyg.o dlbrfg.o dsbein1.o dscgst.o dstebz2.o dsyevx2.o dsyr2m.o dsyrb4.o dsyrb5l.o dsyrdt4.o dsywyv.o dsyxev4.o dvbes1.o eisps.o errclr.o errflg.o forfhs.o gaunt1.o gaunt2.o gbass.o gtfnam.o hamilt.o hns.o horb.o inikpt.o inilpw.o lapw1.o latgen.o lmsort.o locdef.o lohns.o lopw.o matmm.o modules.o nn.o outerr.o outwinb.o prtkpt.o prtres.o pzheevx16.o rdswar.o rint13.o rotate.o rotdef.o seclit.o seclr4.o seclr5.o select.o service.o setkpt.o setwar.o sphbes.o stern.o SymmRot.o tapewf.o ustphx.o vectf.o warpin.o wfpnt.o wfpnt1.o ylm.o zhcgst.o zheevx2.o zher2m.o jacdavblock.o make_albl.o global2local.o par_syrk.o my_dsygst.o refblas_dtrsm.o seclit_par.o pdsyevx17.o pdstebz17.o pdgetri_my.o pzgetri_my.o W2kutils.o W2kinit.o -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -L/opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64 -pthread -L/opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64 /opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_blas95_lp64.a /opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_lapack95_lp64.a -lmkl_scalapack_lp64 -lmkl_cdft_core -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -openmp -lpthread -lm -L/opt/local/fftw3/lib/ -lfftw3_mpi -lfftw3 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread make[1]: Leaving directory `/home/matstud/Wien2K_12_1/SRC_lapw1' Copying programs SRC_lapw1/lapw1 SRC_lapw1/lapw1c SRC_lapw1/lapw1_mpi SRC_lapw1/lapw1c_mpi done. Compile time errors (if any) were: On Aug 24, 2012, at 11:59 PM, Peter Blaha wrote: > To make this comment more clear: > > You did not tell us which command you are using for MPF (parallel compiler). > It is not always mpif90 (as this could use some other compiler or mpi) > it could be mpiifort or something else. > > Then check with "which
[Wien] Fwd: problem with display of SCF results with Wi2ek version 8
Did you read the post: http://zeus.theochem.tuwien.ac.at/pipermail/wien/2010-August/013498.html and try changing "set data style" to "set style data" in the scripts? On 8/28/2012 12:16 AM, Muhammad Sajjad wrote: > Thank you prof. > could you let me know the solution to this problem? i have checked > mailing list but unfortunately i can not solve it. > > On 8/27/12, Peter Blaha wrote: >> Some graphics options of old versions of WIEN2k are not compatible with new >> gnuplot versions. >> >> There were several posts on the mailing list describing these problems. >> >> Am 27.08.2012 06:03, schrieb Muhammad Sajjad: >>> Respected Group Members >>> I am running wien version 8 on a machine of type Dell Core I5 Desktop >>> with operating system FEDORA17 (64 BIT) , fortran compiler >>> "intel_fortran_composer_xe_2011_lin". The purpose of my calculations >>> is to get quantity ELECTRON DENSITY (ED) and DOS. I have completed SCF >>> but when i try to get ED & DOS then the plots do not appear.what does >>> happen there, i have attached it herewith the mail. please see the >>> attachment. even though i have installed gnuplot with command yum >>> install gnuplot. >>> Also when i run SCF with 11 version then it works but i want to use 8 >>> version as i have some problems with version 11. Please help me in >>> this regard. In advance, thanks a lot. >>> >>> Kind Regards >>> M. Sajjad >>> >>> >>> >>> ___ >>> Wien mailing list >>> Wien at zeus.theochem.tuwien.ac.at >>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >>> >> -- >> - >> Peter Blaha >> Inst. Materials Chemistry, TU Vienna >> Getreidemarkt 9, A-1060 Vienna, Austria >> Tel: +43-1-5880115671 >> Fax: +43-1-5880115698 >> email: pblaha at theochem.tuwien.ac.at >> - >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >
