Hi Nick, Please find the attachment for the same . I have included both building and install .
On Thu, Apr 23, 2015 at 10:25 PM, Nick Papior Andersen <[email protected] > wrote: > There should be another error message associated with the python > installation. > Please provide that. > > I.e. try and reinstall inelastica, but pipe the output (plus stderr) to a > file and send that file. > > To pipe stderr to stdout do: > python setup.py install 2>&1 > debug.out > > > > 2015-04-23 22:18 GMT+02:00 ganesh sivaraman <[email protected]>: > >> Hi, >> >> I have this strange error . I don't quiet understand it . Isee that new >> pyTBT has pdos capability. But when i changed to the latest snapshot of >> inelastic i have started to get the following error. >> >> Problems encountered with F90helpers.so >> >> Falling back on a pure python (slower) implementation >> >> Try compiling manually following these steps: >> >> $ cd Inelastica/package/F90 >> >> $ source compile.bat (or compile_alternative.bat) >> >> $ cp F90helpers.so <python>/site-packages/Inelastica/ >> >> >> >> >> I went to this folder and completed this procedure and placed the two >> files in right path and sourced then. still it does not go away . Plus i >> have lapack and boas routines that compiled well for siesta . This is >> rather weird. >> >> Any hints ? >> >> >> >> On Wed, Apr 22, 2015 at 10:51 PM, ganesh sivaraman <[email protected] >> > wrote: >> >>> Thanks all. I will try >>> >>> On Tue, Apr 21, 2015 at 8:54 PM, Magnus Paulsson <[email protected] >>> > wrote: >>> >>>> Try: >>>> pyTBT —help >>>> >>>> (SVN-version of Inelastica) >>>> >>>> This is the python version of tbtrans. Thomas has added a lot of PDOS >>>> calculations and the output files should >>>> be directly readable by xmgrace. I haven’t looked at PDOS myself so I >>>> don’t remember the details. >>>> >>>> -Magnus >>>> >>>> ----------------------------------------------- >>>> Magnus Paulsson >>>> Assistant Professor >>>> Dept. of Physics and Electrical Engineering >>>> Linnaeus University >>>> Phone: +46-480-446308 >>>> Mobile: +46-70-6942987 >>>> >>>> On 21 Apr 2015, at 18:46, ganesh sivaraman <[email protected]> >>>> wrote: >>>> >>>> Hi Nick , >>>> >>>> I am quiet familiar with EIgenchannels tools and --help for that was >>>> always helpful . Inelastica does say its for IETS. There are some flags >>>> similar to eingenchannels , when i tried the --help for inelastic . But i >>>> was not quiet sure about outputs. Its rather confusing unlike >>>> eigenchannels . >>>> >>>> Even some publications using this would have been very helpful . >>>> Please let me know >>>> >>>> >>>> On Tue, Apr 21, 2015 at 11:16 AM, Nick Papior Andersen < >>>> [email protected]> wrote: >>>> >>>>> Have you tried using the --help flag on the commands in Inelastica? >>>>> They are actually pretty helpful. >>>>> >>>>> 2015-04-21 9:40 GMT+02:00 ganesh sivaraman <[email protected]>: >>>>> >>>>>> Hi, >>>>>> >>>>>> I saw that Inelastica has the capability of give PDOS . Does any >>>>>> one have experience how to do this ? >>>>>> >>>>>> T&R, >>>>>> >>>>>> Ganesh Sivaraman >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Kind regards Nick >>>>> >>>> >>>> >>>> >>> >> > > > -- > Kind regards Nick >
ATLAS version 3.10.1 built by abuild on Sun Oct 27 02:09:10 UTC 2013: UNAME : Linux build16 3.4.6-2.10-xen #1 SMP Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux INSTFLG : -1 0 -a 1 -l 1 ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_HAMMER -DATL_CPUMHZ=2210 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_3DNow -DATL_USE64BITS -DATL_GAS_x8664 F2CDEFS : -DAdd_ -DF77_INTEGER=int -DStringSunStyle CACHEEDGE: 524288 F77 : /usr/bin/gfortran-4.8, version GNU Fortran (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC SMC : /usr/bin/gcc-4.8, version gcc-4.8 (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC SKC : /usr/bin/gcc-4.8, version gcc-4.8 (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "Inelastica.F90helpers" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. adding 'build/src.linux-x86_64-2.7/Inelastica/F90helpers-f2pywrappers2.f90' to sources. building extension "Inelastica.F90_lapack" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. building data_files sources build_src: building npy-pkg config files running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_ext running build_scripts ganesh@ibex:/data/data/ganesh/Software/inelastica> python setup.py install ATLAS version 3.10.1 built by abuild on Sun Oct 27 02:09:10 UTC 2013: UNAME : Linux build16 3.4.6-2.10-xen #1 SMP Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux INSTFLG : -1 0 -a 1 -l 1 ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_HAMMER -DATL_CPUMHZ=2210 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_3DNow -DATL_USE64BITS -DATL_GAS_x8664 F2CDEFS : -DAdd_ -DF77_INTEGER=int -DStringSunStyle CACHEEDGE: 524288 F77 : /usr/bin/gfortran-4.8, version GNU Fortran (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC SMC : /usr/bin/gcc-4.8, version gcc-4.8 (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC SKC : /usr/bin/gcc-4.8, version gcc-4.8 (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "Inelastica.F90helpers" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. adding 'build/src.linux-x86_64-2.7/Inelastica/F90helpers-f2pywrappers2.f90' to sources. building extension "Inelastica.F90_lapack" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. building data_files sources build_src: building npy-pkg config files running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_ext running build_scripts running install_lib creating /usr/lib64/python2.7/site-packages/Inelastica error: could not create '/usr/lib64/python2.7/site-packages/Inelastica': Permission denied ganesh@ibex:/data/data/ganesh/Software/inelastica> python setup.py install --user ATLAS version 3.10.1 built by abuild on Sun Oct 27 02:09:10 UTC 2013: UNAME : Linux build16 3.4.6-2.10-xen #1 SMP Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux INSTFLG : -1 0 -a 1 -l 1 ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_HAMMER -DATL_CPUMHZ=2210 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_3DNow -DATL_USE64BITS -DATL_GAS_x8664 F2CDEFS : -DAdd_ -DF77_INTEGER=int -DStringSunStyle CACHEEDGE: 524288 F77 : /usr/bin/gfortran-4.8, version GNU Fortran (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC SMC : /usr/bin/gcc-4.8, version gcc-4.8 (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC SKC : /usr/bin/gcc-4.8, version gcc-4.8 (SUSE Linux) 4.8.1 20130909 [gcc-4_8-branch revision 202388] SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -msse3 -m64 -fPIC /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "Inelastica.F90helpers" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. adding 'build/src.linux-x86_64-2.7/Inelastica/F90helpers-f2pywrappers2.f90' to sources. building extension "Inelastica.F90_lapack" sources f2py options: [] adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.7' to include_dirs. building data_files sources build_src: building npy-pkg config files running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_ext running build_scripts running install_lib creating /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/WriteXMGR.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/Symmetry.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/__init__.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/VaspIO.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/pyTBT.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/SupercellPhonons.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/EigenChannels.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/STM.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/NEB.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/MiscMath.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/Kmesh.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/SetupRuns.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/BandStruct.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/PhysicalConstants.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/ValueCheck.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/Inelastica.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/WriteNetCDF.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/NEGF.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/SiestaIO.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/CommonFunctions.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/Phonons.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/MakeGeom.py -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/F90helpers.so -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica copying build/lib.linux-x86_64-2.7/Inelastica/F90_lapack.so -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/WriteXMGR.py to WriteXMGR.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/Symmetry.py to Symmetry.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/__init__.py to __init__.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/VaspIO.py to VaspIO.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/pyTBT.py to pyTBT.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/SupercellPhonons.py to SupercellPhonons.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/EigenChannels.py to EigenChannels.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/STM.py to STM.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/NEB.py to NEB.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/MiscMath.py to MiscMath.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/Kmesh.py to Kmesh.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/SetupRuns.py to SetupRuns.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/BandStruct.py to BandStruct.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/PhysicalConstants.py to PhysicalConstants.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/ValueCheck.py to ValueCheck.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/Inelastica.py to Inelastica.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/WriteNetCDF.py to WriteNetCDF.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/NEGF.py to NEGF.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/SiestaIO.py to SiestaIO.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/CommonFunctions.py to CommonFunctions.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/Phonons.py to Phonons.pyc byte-compiling /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/MakeGeom.py to MakeGeom.pyc running install_scripts copying build/scripts.linux-x86_64-2.7/Inelastica -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/EigenChannels -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/pyTBT -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/geom2geom -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/geom2zmat -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/Bandstructures -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/siesta_cleanup -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/STMimage -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/Vasp2Siesta -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/bands2xmgr -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/Phonons -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/NEB -> /home/ganesh/.local/bin copying build/scripts.linux-x86_64-2.7/grid2grid -> /home/ganesh/.local/bin changing mode of /home/ganesh/.local/bin/Inelastica to 755 changing mode of /home/ganesh/.local/bin/EigenChannels to 755 changing mode of /home/ganesh/.local/bin/pyTBT to 755 changing mode of /home/ganesh/.local/bin/geom2geom to 755 changing mode of /home/ganesh/.local/bin/geom2zmat to 755 changing mode of /home/ganesh/.local/bin/Bandstructures to 755 changing mode of /home/ganesh/.local/bin/siesta_cleanup to 755 changing mode of /home/ganesh/.local/bin/STMimage to 755 changing mode of /home/ganesh/.local/bin/Vasp2Siesta to 755 changing mode of /home/ganesh/.local/bin/bands2xmgr to 755 changing mode of /home/ganesh/.local/bin/Phonons to 755 changing mode of /home/ganesh/.local/bin/NEB to 755 changing mode of /home/ganesh/.local/bin/grid2grid to 755 running install_data creating /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/PBS copying PBS/RUN.OS.pbs -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/PBS copying PBS/RUN.py.pbs -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/PBS copying PBS/RUN.TS.pbs -> /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/PBS running install_egg_info Writing /home/ganesh/.local/lib/python2.7/site-packages/Inelastica-1.2-py2.7.egg-info running install_clib customize UnixCCompiler
