Re: [Wien] errors in lapw0 and lapw1 - parallel mode compilation
Google found some info here: https://software.intel.com/en-us/forums/topic/485528 You are mixing MKL libraries for the x86-64 target in R_LIB with MKL libraries targeting the Intel Phi (MIC) co-processor in RP_LIB (those in $MKLROOT/lib/mic/). Are you really targeting the Intel Phi co-processor? If not, you need to remove /mic/ from your RP_LIB library paths. If yes, I suspect you need to make use of the MKL link line advisor (https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor) to set some more options (there is at least a -mmic compiler directive that you would need to set). -- Eamon McDermott, M.Sc. Institute of Materials Chemistry, TU Wien eamon.mcderm...@tuwien.ac.at Office: +43 (1) 58801-165304 Scheduling: http://doodle.com/eamon.mcdermott On October 9, 2014 at 5:44:34 AM, Yocefu Hattori (yhattor...@gmail.commailto:yhattor...@gmail.com) wrote: Dear Wien2k users, I'm having problems during compilation of lapw0 and lapw1 in parallel mode. As you can see below there are errors in incompatibility with 32bit, but I installed the ifort (intel composer xe 2013 sp1) compiler in 64 bit. My settings: MKLROOT=/opt/intel/composer_xe_2013_sp1.2.144/mkl MKL_TARGET_ARCH=intel64 Compiler options: -I$(MKLROOT)/include -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io F FFTW options: -DFFTW3 -I/opt/fftw3/include L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/intel64 -pthread P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread FL FFTW_LIBS: /opt/fftw3/lib/libfftw3_mpi.a /opt/fftw3/lib/libfftw3.a RP RP_LIB(SCALAPACK+PBLAS): $(MKLROOT)/lib/mic/libmkl_scalapack_lp64.a -Wl,--start-group $(MKLROOT)/lib/mic/libmkl_intel_lp64.a $(MKLROOT)/lib/mic/libmkl_core.a $(MKLROOT)/lib/mic/libmkl_sequential.a -Wl,--end-group $(MKLROOT)/lib/mic/libmkl_blacs_intelmpi_lp64.a -lpthread -lm FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io MP MPIRUN commando : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ Compile Errors: Compile time errors (if any) were: SRC_lapw0/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(dftierrorclass_lp64.o)' is incompatible with i386:x86-64 output SRC_lapw0/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(dfti_error_class_external.o)' is incompatible with i386:x86-64 output SRC_lapw0/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(_knc_transfer_ipp_mkl_error.o)' is incompatible with i386:x86-64 output SRC_lapw0/compile.msg:make[1]: *** [lapw0_mpi] Error 1 SRC_lapw0/compile.msg:make: *** [para] Error 2 SRC_lapw1/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(vml_error_iface.o)' is incompatible with i386:x86-64 output SRC_lapw1/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(vml_errors.o)' is incompatible with i386:x86-64 output SRC_lapw1/compile.msg:make[1]: *** [lapw1_mpi] Error 1 SRC_lapw1/compile.msg:make: *** [rp] Error 2 SRC_lapw1/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(vml_error_iface.o)' is incompatible with i386:x86-64 output SRC_lapw1/compile.msg:ld: k1om architecture of input file `/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(vml_errors.o)' is incompatible with i386:x86-64 output SRC_lapw1/compile.msg:make[1]: *** [lapw1c_mpi] Error 1 SRC_lapw1/compile.msg:make: *** [cp] Error 2 I had those messages to: fft_modules.o: In function `fftw_parallel_mp_prepare_parallel_ffts_': fft_modules.F:(.text+0x41): undefined reference to `fftw_mpi_init' fft_modules.F:(.text+0xbe): undefined reference to `fftw_mpi_local_size_3d_f03' fft_modules.F:(.text+0xcd): undefined reference to `fftw_alloc_complex' fft_modules.o: In function `fftw_parallel_mp_c3fft_': fft_modules.F:(.text+0x11d4): undefined reference to `fftw_mpi_execute_dft' fft_modules.F:(.text+0x2523): undefined reference to `fftw_mpi_execute_dft' fft_modules.F:(.text+0x46f1): undefined reference to `fftw_mpi_plan_dft_3d_f03' fft_modules.F:(.text+0x5195): undefined reference to `fftw_mpi_plan_dft_3d_f03' ld: /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(_knc_Iotensor.o)(.text+0xb99): unresolvable R_X86_64_PLT32 relocation against symbol `fflush@@GLIBC_2.2.5' ld: final link failed: Nonrepresentable section on output make[1]: *** [lapw0_mpi] Error 1 make[1]: Leaving directory `/home/yhattori/WIEN2k_13/SRC_lapw0' make: *** [para] Error 2 Copying programs SRC_lapw0/lapw0 done. For fftw3 (3.3.3) installation I used configure
Re: [Wien] lapw2 error
You must run add -up and -dn to your command. Regards, -- Eamon On Mar 28, 2014, at 10:15 AM, ben amara imen imen.benama...@gmail.com wrote: Hello, I'm working on a magnetic compound . I do the SCF (runsp_lapw) and it went well. Then to calculate the DOS, I executed the command ''x lapw2-qtl'' but I have this error in lapw2 !! : Error in LAPW2 'LAPW2' -can't open unit 18 'LAPW2'filename : case.vsp 'LAPW2' Status: old form : formatted what can I do to overcome my probleme , can someone helps me please and Thanks in advance Best Regards ___ 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
Re: [Wien] Bi2Se3 atomic positions in wien2k structure file.
Crystallography.nethttp://Crystallography.net appears to have the structure you want: http://www.crystallography.net/9011965.html Simply download the .CIF file and use 'cif2struct'. Regards, -- Eamon McDermott, M.Sc. Institute of Materials Chemistry, TU Wien eamon.mcderm...@tuwien.ac.atmailto:eamon.mcderm...@tuwien.ac.at Office: +43 (1) 58801-165304 Scheduling: http://doodle.com/eamon.mcdermott On Feb 6, 2014, at 3:35 PM, Naseem Hassan rahesk...@gmail.commailto:rahesk...@gmail.com wrote: Dear Users, This is strange but what else I can do except reporting it. I am unable to download the attachment from the fallowing email which is in the archive (probably never attached). http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08497.html Kindly suggest me how can I make Bi2Se3 structure file ? The space group is space group R3m (166)and structure is hexagonal. But I do not know how many atoms should I generate for structure file and what are the positions for respective atoms ? I would appreciate if some one help how to find position from the official link below, in this way I will learn alot. http://cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=166grha=hexagonal Best wishes Naseem (A beginner in wien2k code) ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.atmailto: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
Re: [Wien] mbj error
Then the problem is exactly as Tomas has described it. If lapw1 is searching for a .vsp file (and not .vspup/.vspdn) then you are running 'run_lapw' when you have initialized for a spin-polarized case. I agree that you should re-start your calculation from a clean directory with only the struct file, and make sure to use 'runsp_lapw' if starting your SCF cycle from the command line. Regards, -- Eamon McDermott PhD student Institute for Materials Chemistry, TU Wien eamon.mcderm...@tuwien.ac.atmailto:eamon.mcderm...@tuwien.ac.at On 2013-08-01, at 8:57 PM, mourad boujnah boujnah.mou...@gmail.commailto:boujnah.mou...@gmail.com wrote: Dear Gavin and Tomas, this is the error in lapw1.error Error in LAPW1 'INILPW' - can't open unit: 18 'INILPW' -filename: ZrO2-Fe.vsp 'INILPW' - status: old form: formatted 'LAPW1' - INILPW aborted unsuccessfully. and this calculation with spin polarized 2013/8/1 Tomas Kana k...@seznam.czmailto:k...@seznam.cz Dear Mourad Boujnah, Just a guess: Do you perform a non-magnetic or a spin polarized calculation? (in your directory you have Ferro-dos) If you initialized your structure as spin-polarized, you should use runsp_lapw instead of run_lapw If this is really the cause of your problem, I would erase everything except struct file and initialize again and then run runsp_lapw Tomas -- Původní zpráva -- Od: mourad boujnah boujnah.mou...@gmail.commailto:boujnah.mou...@gmail.com Datum: 1. 8. 2013 Předmět: [Wien] mbj error Dear Wien2k Users, I am using Wien2k 13 version and i am performing mBj calculations. In the firt step when I give the command run_lapw -i 1 -NI The following error appeared. oujnah@boujnah:~/WIEN2k/Boujnah/TM-ZrO2/Ferro-dos/ZrO2-Fe$ run_lapw -i 1 -NI hup: Command not found. LAPW0 END LAPW1 - Error stop error Please can you help me to overcome this problem .? Cordialy -- Mourad BOUJNAH PhD Student in laboratory of magnetism and physics of high energy Faculty of Sciences in Rabat - Morocco Tel: +212 677316706 Email: boujnah.mou...@gmail.commailto:boujnah.mou...@gmail.com Research is to see what everybody else has seen, and to think what nobody else has thought ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.atmailto: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 -- Mourad BOUJNAH PhD Student in laboratory of magnetism and physics of high energy Faculty of Sciences in Rabat - Morocco Tel: +212 677316706 Email: boujnah.mou...@gmail.commailto:boujnah.mou...@gmail.com Research is to see what everybody else has seen, and to think what nobody else has thought ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.atmailto: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
Re: [Wien] error in running the x opticc
no space left on device You have run out of disk space on the device containing your output directory, or for some other reason the process is unable to write to the disk (such as NFS issues). Best regards, -- Eamon McDermott, M.Sc. Institute of Materials Chemistry, TU Wien eamon.mcderm...@tuwien.ac.atmailto:eamon.mcderm...@tuwien.ac.at Office: +43 (1) 58801-165304 Scheduling: http://doodle.com/eamon.mcdermott On 2013-04-07, at 12:08 PM, ben abdallah houda bhoud...@yahoo.frmailto:bhoud...@yahoo.fr wrote: Dear Wien2k users, I am trying to calculate the magneto-optical properties of GaMnAsP. For this I have done in the first step the calculation SO then I completed all the steps to start the stage optics, using the x opticc -so -up. This step has been discontinued and I found the following message: forrtl: no space left on device forrtl: severe (38): error during write, unit 3, file /home/houda/WIEN2K/ GaMnAsP.symmatup error: command /homr/houda/wien2kpackages/ opticc upoptic.def failed I want to know: what this message means and how I can fix this error. I really need to solve this as I am in the final stage of my work. Thank you for your answer in advance. I am very grateful Dr. Houda Ben Abdallah. Departement of Physics, Laboratory of Condensed Matter (LPMC). Faculty of Sciences, Tunis. Tunisia ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.atmailto:Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] error in lapw2 - parallel
I recommend checking for NaN's in your Cu.scf0 file. This behaviour looks similar to what I've seen before in some cases when using the broken FFT library in the early 12.1 release. It can be fixed for the serial mode lapw0 by adding -DFFTW3 or -DFFTW2 to FOPT and linking to an fftw in R_LIBS. -- Eamon McDermott, M.Sc. Institute of Materials Chemistry, TU Wien eamon.mcdermott at tuwien.ac.at Office: +43 (1) 58801-165304 Scheduling: http://doodle.com/eamon.mcdermott On Fri, 2013-03-22 at 08:41 -0400, Mathrubutham Rajagopalan wrote: I am waiting for your reply Raja Sent from my iPad On Mar 22, 2013, at 5:21 AM, Lyudmila Dobysheva lyuka17 at mail.ru wrote: The order of your actions should be another: 1. Make a fresh directory. 2. Make in terminal the commands by hand x lapw0 x lapw1 -c -p x lapw2 -c -p and send us the output in terminal and error files if nonzero 3. Check the output of lapw1: *.scf1 and *.output1 Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 442118 (home), 218988(office), 722529(Fax) E-mail: lyu at ftiudm.ru lyuka17 at mail.ru (office) lyuka17 at gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://fti.udm.ru/content/view/25/103/lang,english/ -- ___ 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
