[Wien] Wien2k installation problem
Fecher, Gerhard
fecher at uni-mainz.de
Fri Jul 17 11:13:10 CEST 2015
Hi Shamik,
your bash.rc should contain something like
(please check the path on yor computer, take the real *vars.sh versions not the symbolic links)
source /opt/intel/composer_xe_2013.5.192/bin/compilervars.sh intel64
source /opt/intel/composer_xe_2013.5.192/mkl/bin/mklvars.sh intel64
or
source /opt/intel/composer_xe_2013.5.192/mkl/bin/intel64/mklvars_intel64.sh
note: Take care that you realy "source" the correct *vars.sh with the correct switch
e.g. the directory /opt/intel/bin will contain probably links to compiler/mkl versions that you don't like to use (always latest installation I guess),
therefore, check carefully were the correct *vars.sh are installed on your computer
the links in /opt/intel/composer_xe_2013 or /opt/intel/composer_xe_2015 may work correctly (but I did NOT check that)
note: above I used the path to the Intel tools on my computer, it might be different on yours
I have both ifort and icc in /opt/intel/composer_xe_2013.5.192/bin/intel64
the name of the compilers is ifort or icc
(the *.cfg files are configuration files if you like to use additional switches, this are not the compilers)
for mic installation, check which *vars.sh you need, maybe you will also need something pointing to the mpi environment
Ciao
Gerhard
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."
====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden
________________________________________
Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von shamik chakrabarti [shamikphy at gmail.com]
Gesendet: Freitag, 17. Juli 2015 09:16
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Wien2k installation problem
Dear Gerhard,
An ifort version, ifort.cfg is there in intel64 directory. Whether ifort and ifort.cfg are same?...Whenever, I set the path for ifort.cfg in .bashrc_profile, and after sourcing it...ifort seems to be installed as can be checked from ifort -v command in terminal....However, when I am logging out..& log in ...ifort seems to be missing with ifort command not found in the terminal. What could be the reason?
Looking forward to your suggestion in this regard.
with regards,
On Fri, Jul 17, 2015 at 12:43 AM, shamik chakrabarti <shamikphy at gmail.com<mailto:shamikphy at gmail.com>> wrote:
Dear Gerhard,
As I have not installed the Composer_xe_2015 version to our server, I don't have any idea whether the installation of intel64 version of ifort was restricted or not, However...I can do one thing: I can install l_fcompxe_2013_sp1.1.106 to our home directory and link the path of ifort and mkl accordingly. As I have installed wien2k with this compiler previously & it contains the intel64 version of ifort, we may not face any problem. At the moment, I think this could be the solution.
Dear Gavin,
Thank you for your suggestions. Yes I will follow those links and try to gain more knowledge of installing wien2k in PHI processor...
Thank you once again.
with regards,
On Thu, Jul 16, 2015 at 8:47 PM, Gavin Abo <gsabo at crimson.ua.edu<mailto:gsabo at crimson.ua.edu>> wrote:
Since you say that the "segmentation fault (core dumped)" error occurs during the running of ifort, you might also want to ask about the error in the Intel Fortran Compiler for Linux* and Mac OS X* forum [ https://software.intel.com/en-us/forum ]. One of the Intel representatives might know if it could caused by the DPD200364057 Fortran Internal Compiler Error when compiling with -openmp or one of the other bugs listed or not listed in the 2015 Composer Edition Compilers Fixes List [ https://software.intel.com/en-us/articles/intel-composer-xe-2015-compilers-fixes-list ].
On 7/16/2015 8:50 AM, Fecher, Gerhard wrote:
Dear Shamik,
- what main processor does your computer have ? (It cannot be XEON PHI as this is a co-processor on some extra card)
- if you compile for the XEON Phi, Wien2k will most probably not work on the main processor of your computer
that is, if you compile it native for the PHI then you have to run it on the PHI
check the Intel manuals and the Intel link advisor for the PHI off-load models and how to use the mic options.
- the XEON PHIs are implemented since the 2013 versions (e.g. parallel_studio_xe_2013) and those have also the emt64 versions
of ifort (in /opt/intel/composer_xe_2013.5.192/bin/intel64), icc, mkl (in /opt/intel/composer_xe_2013.5.192/mkl/lib/intel64) etc.
- the composer_xe_2015_090 has both, intel_64 and intel64_mic for ifort and icc (or did you restrict the installation somehow ?)
(interesting I don't have a special mic directory for the mkl of xe_2015, but may be I just didn't install it
because the mic directory contains libraries only for native PHI programs)
Ciao
Gerhard
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."
====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden
________________________________________
Von: wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at> [wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>] im Auftrag von shamik chakrabarti [shamikphy at gmail.com<mailto:shamikphy at gmail.com>]
Gesendet: Donnerstag, 16. Juli 2015 14:42
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Wien2k installation problem
Dear Gerhard & Gavin,
The compiler ifort is available only in mic directory for composer_xe_2015.0.090, and that's why we have also set the path of mkl to mic as otherwise we are getting an error of not finding mkl libs by X86_64-K1om-linux-ld:
However, after setting the path of mkl to mic, there were no such error appeared except,
segmentation fault (core dumped).
This error is again appeared due to ifort (& not by gcc)
The appearance of error is independent of whether we have set $(FOPT) or not to Linker Flags.
All the -pthread are converted to -lpthread in the OPTION
However, the error segmentation fault (core dumped) is still appearing after compiling & this is the only one error we are left with.
Do you think that if we use some older version of compiler in which "ifort" is available in intel64...then the problem may be solved?...
However, I have no idea that whether the older version of compiler is compatible with "XEON PHI" processor?
Looking forward to your suggestion in this regard.
with regards,
On Wed, Jul 15, 2015 at 8:49 PM, Gavin Abo <gsabo at crimson.ua.edu<mailto:gsabo at crimson.ua.edu><mailto:gsabo at crimson.ua.edu<mailto:gsabo at crimson.ua.edu>>> wrote:
Dear Gerhard and Shamik,
Ok, sorry, I did not think too much into it.
In siteconfig,
1) selected "S specify a system" and "I Linux (Intel ifort compiler (12.0 and later) + mkl )"
2) selected "O specify compiler options, BLAS and LAPACK", and it gave:
Recommended options for system linuxifc are:
Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io
Linker Flags: $(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread
Preprocessor flags: '-DParallel'
R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread
I knew that these recommended 64 bit settings have worked fine for me on different Linux operating systems. Until you mentioned it, I did not know that -pthread could be safely dropped from the Linker Flags.
Thanks,
Gavin
why -pthread instead of -lpthread ? The threading library is libpthread and should be linked with -lpthread !
I remembre that I made some ten years ago the remark on that: On SUSE systems (at thae time it was 9.2 and older) one can have a very comfortable setup of the linker
such that it finds the standart libraries by itself. You can check it if you remove the -pthread switch from the linker line and find that Wien2k is still linked correctly.
If not then you may use ldconfig to make your linker environment more comfortable.
Below I do not understand why the linker should need the compiler options (LDFLAGS:$(FOPT)) ??
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Shamik Chakrabarti
Senior Research Fellow
Dept. of Physics & Meteorology
Material Processing & Solid State Ionics Lab
IIT Kharagpur
Kharagpur 721302
INDIA
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SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
--
Shamik Chakrabarti
Senior Research Fellow
Dept. of Physics & Meteorology
Material Processing & Solid State Ionics Lab
IIT Kharagpur
Kharagpur 721302
INDIA
--
Shamik Chakrabarti
Senior Research Fellow
Dept. of Physics & Meteorology
Material Processing & Solid State Ionics Lab
IIT Kharagpur
Kharagpur 721302
INDIA
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