Re: [Wien] How to do Site Configuration In Ubuntu 12.04
Dear Sir Thank you sir as you suggest i have done now i'm getting nrl@nrl-Vostro-220s-Series:~$ cd WIEN2k nrl@nrl-Vostro-220s-Series:~/WIEN2k$ ./siteconfig_lapw * *W I E N* * site configuration * * Last configuration: Fri Apr 5 13:09:11 IST 2013 Wien Version: WIEN2k_12.1 (Release 22/7/2012) System: linuxifc S specify a system C specify compiler O specify compiler options, BLAS and LAPACK P configure Parallel execution D Dimension Parameters R Compile/Recompile U Update a package L Perl path (if not in /usr/bin/perl) Q Quit Selection: O ** * Specify compiler options * ** PLEASE NOTE: Best performance can be obtained with processor specific options. Very important for speed-up is a optimized BLAS (like mkl, essl, ..), or at least the GOTO- or ATLAS-BLAS instead of the simple -lblas_lapw For more info see http://www.wien2k.at/reg_user/faq searching You have the following mkl libraries in /home/nrl/intel/composer_xe_2013.3.163/mkl : /home/nrl/intel/composer_xe_2013.3.163/mkl/lib/ia32/libmkl_gf.so /home/nrl/intel/composer_xe_2013.3.163/mkl/lib/ia32/libmkl_blas95.a /home/nrl/intel/composer_xe_2013.3.163/mkl/lib/ia32/libmkl_vml_p4p.so . . . http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ Recommended options for system linuxifc are: Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread Preprocessor flags: '-DParallel' R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread Current settings: O Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback L Linker Flags:$(FOPT) -L/opt/intel/composerxe/mkl/lib/ia32 -pthread P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread S Save and Quit Q Quit abandon changes To change an item select option. Selection: After i select R (compile all) than getting these errors /lib/ia32 -pthread lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread ifort: error #10236: File not found: 'lmkl_lapack95' make[1]: *** [filtvec] Error 1 make[1]: Leaving directory `/home/nrl/WIEN2k/SRC_filtvec' make: *** [real] Error 2 On Fri, Apr 5, 2013 at 11:15 AM, Peter Blaha pbl...@theochem.tuwien.ac.atwrote: You say: I have installed ifort + mkl Where did you install it ??? (in which directory) ??? It seems, siteconfig cannot find it in the default /opt/intel/ path Once you know, where it is, change into the installation directory and look for the configuration script compilervars.sh. Find out the complete pathname and put a line as suggested previously into ~/.bashrc source your-path/compilervars.sh intel64 then logout/login again and check: which ifort echo $MKLROOT Am 05.04.2013 06:47, schrieb vishal jain: I do as you mention but observed same error SRC_sumhfpara/compile.msg:**make: *** [complex] Error 2 SRC_sumpara/compile.msg:make: *** [errclr.o] Error 127 SRC_supercell/compile.msg:**make: *** [supercell.o] Error 127 SRC_symmetry/compile.msg:make: *** [symmetry.o] Error 127 SRC_symmetso/compile.msg:make: *** [symmetso.o] Error 127 SRC_telnes3/compile.msg:make: *** [modules.o] Error 127 SRC_tetra/compile.msg:make: *** [reallocate.o] Error 127 SRC_trig/compile.msg:make: *** [rhomb_in5.o] Error 127 SRC_txspec/compile.msg:make: *** [reallocate.o] Error 127 SRC_vecpratt/compile.msg:make[**1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [real] Error 2 SRC_vecpratt/compile.msg:make[**1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [complex] Error 2 SRC_structeditor/SRC_**ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_**readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_**struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_**structgen/compile.msg:make: *** [module.o] Error 127 in P configure Parallel execution i choose * Configure parallel execution * These options are stored in parallel_options of WIENROOT You can change them later also manually. Do you use ONLY a shared memory parallel architecture (ONE single multi-core node) ? On shared memory system it is normally better to start jobs in
Re: [Wien] How to do Site Configuration In Ubuntu 12.04
You missed - sign It should be -lmkl_lapack95 On Fri, Apr 5, 2013 at 3:56 AM, vishal jain vjain...@gmail.com wrote: Dear Sir Thank you sir as you suggest i have done now i'm getting nrl@nrl-Vostro-220s-Series:~$ cd WIEN2k nrl@nrl-Vostro-220s-Series:~/WIEN2k$ ./siteconfig_lapw * *W I E N* * site configuration * * Last configuration: Fri Apr 5 13:09:11 IST 2013 Wien Version: WIEN2k_12.1 (Release 22/7/2012) System: linuxifc S specify a system C specify compiler O specify compiler options, BLAS and LAPACK P configure Parallel execution D Dimension Parameters R Compile/Recompile U Update a package L Perl path (if not in /usr/bin/perl) Q Quit Selection: O ** * Specify compiler options * ** PLEASE NOTE: Best performance can be obtained with processor specific options. Very important for speed-up is a optimized BLAS (like mkl, essl, ..), or at least the GOTO- or ATLAS-BLAS instead of the simple -lblas_lapw For more info see http://www.wien2k.at/reg_user/faq searching You have the following mkl libraries in /home/nrl/intel/composer_xe_2013.3.163/mkl : /home/nrl/intel/composer_xe_2013.3.163/mkl/lib/ia32/libmkl_gf.so /home/nrl/intel/composer_xe_2013.3.163/mkl/lib/ia32/libmkl_blas95.a /home/nrl/intel/composer_xe_2013.3.163/mkl/lib/ia32/libmkl_vml_p4p.so . . . http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ Recommended options for system linuxifc are: Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread Preprocessor flags: '-DParallel' R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread Current settings: O Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback L Linker Flags:$(FOPT) -L/opt/intel/composerxe/mkl/lib/ia32 -pthread P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread S Save and Quit Q Quit abandon changes To change an item select option. Selection: After i select R (compile all) than getting these errors /lib/ia32 -pthread lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread ifort: error #10236: File not found: 'lmkl_lapack95' make[1]: *** [filtvec] Error 1 make[1]: Leaving directory `/home/nrl/WIEN2k/SRC_filtvec' make: *** [real] Error 2 On Fri, Apr 5, 2013 at 11:15 AM, Peter Blaha pbl...@theochem.tuwien.ac.at wrote: You say: I have installed ifort + mkl Where did you install it ??? (in which directory) ??? It seems, siteconfig cannot find it in the default /opt/intel/ path Once you know, where it is, change into the installation directory and look for the configuration script compilervars.sh. Find out the complete pathname and put a line as suggested previously into ~/.bashrc source your-path/compilervars.sh intel64 then logout/login again and check: which ifort echo $MKLROOT Am 05.04.2013 06:47, schrieb vishal jain: I do as you mention but observed same error SRC_sumhfpara/compile.msg:**make: *** [complex] Error 2 SRC_sumpara/compile.msg:make: *** [errclr.o] Error 127 SRC_supercell/compile.msg:**make: *** [supercell.o] Error 127 SRC_symmetry/compile.msg:make: *** [symmetry.o] Error 127 SRC_symmetso/compile.msg:make: *** [symmetso.o] Error 127 SRC_telnes3/compile.msg:make: *** [modules.o] Error 127 SRC_tetra/compile.msg:make: *** [reallocate.o] Error 127 SRC_trig/compile.msg:make: *** [rhomb_in5.o] Error 127 SRC_txspec/compile.msg:make: *** [reallocate.o] Error 127 SRC_vecpratt/compile.msg:make[**1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [real] Error 2 SRC_vecpratt/compile.msg:make[**1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [complex] Error 2 SRC_structeditor/SRC_**ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_**readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_**struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_**structgen/compile.msg:make: *** [module.o] Error 127 in P configure Parallel execution i choose * Configure parallel execution * These options are stored in parallel_options of WIENROOT You can change
Re: [Wien] How to do Site Configuration In Ubuntu 12.04
Try changing the Linker and R_LIB lines to: Linker Flags:$(FOPT) -L/opt/intel/composerxe/mkl/lib/ia32 -pthread R_LIB (LAPACK+BLAS):-lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread On 4/4/2013 9:52 PM, vishal jain wrote: Dear Sir I found error on compiling (R=Compile and Recompile) . SRC_structeditor/SRC_ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_structgen/compile.msg:make: *** [module.o] Error 127 In site configration i choose following comands S specify a system I choose I(ifort + MKL because i have installed l_mkl_11.0.2.146 and l_fcompxe_2013.3.163) ) C i choose ifort + cc O shown below how to define path * *W I E N * * site configuration * * Last configuration: Fri Apr 5 09:14:26 IST 2013 Wien Version: WIEN2k_12.1 (Release 22/7/2012) System: linuxifc S specify a system C specify compiler O specify compiler options, BLAS and LAPACK P configure Parallel execution D Dimension Parameters R Compile/Recompile U Update a package L Perl path (if not in /usr/bin/perl) Q Quit Selection: O ** * Specify compiler options * ** PLEASE NOTE: Best performance can be obtained with processor specific options. Very important for speed-up is a optimized BLAS (like mkl, essl, ..), or at least the GOTO- or ATLAS-BLAS instead of the simple -lblas_lapw For more info see http://www.wien2k.at/reg_user/faq searching I could not find the mkl-library because MKLROOT is not defined. Please check whether mkl is installed at all and where (mkl is included in new ifort versions, see www.intel.com http://www.intel.com ) Without mkl you should install the GOTO-blas or you must use the blas_lapw library (performance loss) Hit Enter to continue Since intel changes the name of the mkl-libraries from version to version, you may find the linking options for the most recent ifort version at http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ Recommended options for system linuxifc are: Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback Linker Flags:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread Preprocessor flags: '-DParallel' R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread Current settings: O Compiler options:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback L Linker Flags:$(FOPT) -pthread -static P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): -lmkl_lapack95_ia32 -lmkl_intel_ia32 -lmkl_intel_thread -lmkl_core -openmp -lpthread S Save and Quit Q Quit abandon changes To change an item select option. Selection: ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
Re: [Wien] How to do Site Configuration In Ubuntu 12.04
I do as you mention but observed same error SRC_sumhfpara/compile.msg:make: *** [complex] Error 2 SRC_sumpara/compile.msg:make: *** [errclr.o] Error 127 SRC_supercell/compile.msg:make: *** [supercell.o] Error 127 SRC_symmetry/compile.msg:make: *** [symmetry.o] Error 127 SRC_symmetso/compile.msg:make: *** [symmetso.o] Error 127 SRC_telnes3/compile.msg:make: *** [modules.o] Error 127 SRC_tetra/compile.msg:make: *** [reallocate.o] Error 127 SRC_trig/compile.msg:make: *** [rhomb_in5.o] Error 127 SRC_txspec/compile.msg:make: *** [reallocate.o] Error 127 SRC_vecpratt/compile.msg:make[1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [real] Error 2 SRC_vecpratt/compile.msg:make[1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [complex] Error 2 SRC_structeditor/SRC_ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_structgen/compile.msg:make: *** [module.o] Error 127 in P configure Parallel execution i choose ** * Configure parallel execution * ** These options are stored in parallel_options of WIENROOT You can change them later also manually. Do you use ONLY a shared memory parallel architecture (ONE single multi-core node) ? On shared memory system it is normally better to start jobs in the background rather than using remote commands. If you select a shared memory system WIEN will by default not use remote shell commands (USE_REMOTE and MPI_REMOTE = 0 in parallel_options) and set the default granularity to 1. You still can override this default granularity in your .machines file. You may also set a specific TASKSET command to bind your executables to a specific core on multicore machines. Shared Memory Architecture? (y/n):y Do you know/need a command to bind your jobs to specific nodes ? (like taskset -c). Enter N / your_specific_command: n On most mpi-2 versions, it is better to start an mpijob on the original machine and not via ssh on a remote system. If you are using mpi2 set MPI_REMOTE to 0 Set MPI_REMOTE to 0 / 1: 0 Do you have MPI and Scalapack installed and intend to run finegrained parallel? (This is usefull only for BIG cases (50 atoms and more / unit cell) and you need to know details about your installed mpi and fftw ) (y/n) n On Fri, Apr 5, 2013 at 9:42 AM, Gavin Abo gs...@crimson.ua.edu wrote: Try changing the Linker and R_LIB lines to: Linker Flags:$(FOPT) -L/opt/intel/composerxe/mkl/lib/ia32 -pthread R_LIB (LAPACK+BLAS):-lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread On 4/4/2013 9:52 PM, vishal jain wrote: Dear Sir I found error on compiling (R=Compile and Recompile) . SRC_structeditor/SRC_ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_structgen/compile.msg:make: *** [module.o] Error 127 In site configration i choose following comands S specify a system I choose I(ifort + MKL because i have installed l_mkl_11.0.2.146 and l_fcompxe_2013.3.163) ) C i choose ifort + cc O shown below how to define path * *W I E N* * site configuration * * Last configuration: Fri Apr 5 09:14:26 IST 2013 Wien Version: WIEN2k_12.1 (Release 22/7/2012) System: linuxifc S specify a system C specify compiler O specify compiler options, BLAS and LAPACK P configure Parallel execution D Dimension Parameters R Compile/Recompile U Update a package L Perl path (if not in /usr/bin/perl) Q Quit Selection: O ** * Specify compiler options * ** PLEASE NOTE: Best performance can be obtained with processor specific options. Very important for speed-up is a optimized BLAS (like mkl, essl, ..), or at least the GOTO- or ATLAS-BLAS instead of the simple -lblas_lapw For more info see http://www.wien2k.at/reg_user/faq searching I could not find the mkl-library because MKLROOT is not defined. Please check whether mkl is installed at all and where (mkl is included in new ifort versions, see www.intel.com ) Without mkl you should install the GOTO-blas or you must use the blas_lapw library (performance loss) Hit Enter to continue Since
Re: [Wien] How to do Site Configuration In Ubuntu 12.04
You say: I have installed ifort + mkl Where did you install it ??? (in which directory) ??? It seems, siteconfig cannot find it in the default /opt/intel/ path Once you know, where it is, change into the installation directory and look for the configuration script compilervars.sh. Find out the complete pathname and put a line as suggested previously into ~/.bashrc source your-path/compilervars.sh intel64 then logout/login again and check: which ifort echo $MKLROOT Am 05.04.2013 06:47, schrieb vishal jain: I do as you mention but observed same error SRC_sumhfpara/compile.msg:make: *** [complex] Error 2 SRC_sumpara/compile.msg:make: *** [errclr.o] Error 127 SRC_supercell/compile.msg:make: *** [supercell.o] Error 127 SRC_symmetry/compile.msg:make: *** [symmetry.o] Error 127 SRC_symmetso/compile.msg:make: *** [symmetso.o] Error 127 SRC_telnes3/compile.msg:make: *** [modules.o] Error 127 SRC_tetra/compile.msg:make: *** [reallocate.o] Error 127 SRC_trig/compile.msg:make: *** [rhomb_in5.o] Error 127 SRC_txspec/compile.msg:make: *** [reallocate.o] Error 127 SRC_vecpratt/compile.msg:make[1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [real] Error 2 SRC_vecpratt/compile.msg:make[1]: *** [vecpratt.o] Error 127 SRC_vecpratt/compile.msg:make: *** [complex] Error 2 SRC_structeditor/SRC_ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_structgen/compile.msg:make: *** [module.o] Error 127 in P configure Parallel execution i choose ** * Configure parallel execution * ** These options are stored in parallel_options of WIENROOT You can change them later also manually. Do you use ONLY a shared memory parallel architecture (ONE single multi-core node) ? On shared memory system it is normally better to start jobs in the background rather than using remote commands. If you select a shared memory system WIEN will by default not use remote shell commands (USE_REMOTE and MPI_REMOTE = 0 in parallel_options) and set the default granularity to 1. You still can override this default granularity in your .machines file. You may also set a specific TASKSET command to bind your executables to a specific core on multicore machines. Shared Memory Architecture? (y/n):y Do you know/need a command to bind your jobs to specific nodes ? (like taskset -c). Enter N / your_specific_command: n On most mpi-2 versions, it is better to start an mpijob on the original machine and not via ssh on a remote system. If you are using mpi2 set MPI_REMOTE to 0 Set MPI_REMOTE to 0 / 1: 0 Do you have MPI and Scalapack installed and intend to run finegrained parallel? (This is usefull only for BIG cases (50 atoms and more / unit cell) and you need to know details about your installed mpi and fftw ) (y/n) n On Fri, Apr 5, 2013 at 9:42 AM, Gavin Abo gs...@crimson.ua.edu mailto:gs...@crimson.ua.edu wrote: Try changing the Linker and R_LIB lines to: Linker Flags:$(FOPT) -L/opt/intel/composerxe/mkl/lib/ia32 -pthread R_LIB (LAPACK+BLAS):-lmkl_lapack95 -lmkl_intel -lmkl_intel_thread -lmkl_core -openmp -lpthread On 4/4/2013 9:52 PM, vishal jain wrote: Dear Sir I found error on compiling (R=Compile and Recompile) . SRC_structeditor/SRC_ncmsymmetry/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_readwrite/compile.msg:make: *** [module.o] Error 127 SRC_structeditor/SRC_struct2mol/compile.msg:make: *** [reallocate.o] Error 127 SRC_structeditor/SRC_structgen/compile.msg:make: *** [module.o] Error 127 In site configration i choose following comands S specify a system I choose I(ifort + MKL because i have installed l_mkl_11.0.2.146 and l_fcompxe_2013.3.163) ) C i choose ifort + cc O shown below how to define path * *W I E N * * site configuration * * Last configuration: Fri Apr 5 09:14:26 IST 2013 Wien Version: WIEN2k_12.1 (Release 22/7/2012) System: linuxifc S specify a system C specify compiler O specify compiler options, BLAS and LAPACK P configure Parallel execution D Dimension Parameters R Compile/Recompile U Update a package L Perl path (if not in /usr/bin/perl) Q Quit Selection: O ** * Specify compiler options *
