[Wien] Compiling for Athlon x2
Pablo de la Mora
delamora at servidor.unam.mx
Wed May 2 21:33:18 CEST 2007
Dear Peter,
Thank you, now it worked well, with the -pthread and the LD_LIBRARY_PATH
There is also a
export OMP_NUM_THREADS=2
Should I uncomment it?
Yours
Pablo
By the way I have some usefull aliases
alias gdis='grep :DIS *.scf'
alias tdis='tail -f *scf | grep :DIS'
alias scf='tail -30 *.scf'
alias gene='grep :ENE *.scf'
alias tene='tail -f *scf | grep :ENE'
alias gk="grep ' K=' *.output1*"
alias tk="tail -f *.output1* | grep ' K='"
alias log='tail -20f :log'
alias day='tail -30 *.dayfile'
alias chard='grep CHAR *.dayfile'
alias ened='grep ENE *.dayfile'
alias fer='grep :FER *.scf'
alias ferc='grep :FER conv/*.scf'
Peter Blaha escribió:
> a) It is well documented and there were several messages in the mailing
> list, that you cannot use static linking with ifort9.x and mkl.
>
> b) After succesfull compilation, you've got a dynamically executable,
> which needs the libraries also at run time. This must be ensured be
> putting a proper LD_LIBRARY_PATH variable. (userconfig even put
> coments into .cshrc/.bashrc, but you have to uncomment this and put the
> proper path names into it.
>
>
> Pablo de la Mora schrieb:
>
>> Dear Chandrika,
>> Thank you for your advise, but there is something funny about the 'intel
>> mkl'; it cannot find lapack64.
>>
>> I tried what you suggested, I explicitly put
>> PATH="$PATH:$WIENROOT:/opt/intel/mkl/9.0/lib/em64t"
>> I modified two files in
>> /etc/ld.so.conf.d
>> mysql-x86_64.conf
>> qt-x86_64.conf
>> in both I put the line
>> /opt/intel/mkl/9.0/lib/em64t
>> the file
>> /opt/intel/mkl/9.0/lib/em64t/libmkl_lapack64.so
>> exists and is not empty.
>>
>> When I make a static compilation:
>>
>> Recommended options for system linuxif8 are:
>> Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip
>> -DINTEL_VML
>> Linker Flags: $(FOPT) -L/opt/intel/mkl/8.0/lib/em64t
>> -lpthread
>> Preprocessor flags: '-DParallel'
>> R_LIB (LAPACK+BLAS): -lmkl_lapack64 -lmkl_em64t -lguide
>>
>> Current settings:
>> O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip
>> -DINTEL_VML
>> L Linker Flags: $(FOPT) -L/opt/intel/mkl/9.0/lib/em64t
>> -lpthread -static
>> P Preprocessor flags '-DParallel'
>> R R_LIB (LAPACK+BLAS): -lmkl_lapack64 -lmkl_em64t -lguide
>>
>> I get:
>> SRC_lapw1/compile.msg-ld: no se puede encontrar -lmkl_lapack64
>> (it cannot find -lmkl_lapack64)
>>
>> if, on the other hand, I compile dinamically I get
>> undefined 'pthread_atfork'
>>
>> but as Peter Blaha suggested I put '-pthread' into the compiling options.
>> In this case I do not get any compiling errors, but when I run the program
>> x lapw1
>> I go back to the original problem, I get:
>> /home/Programas/WIEN2k/lapw1: error while loading shared libraries:
>> libmkl_lapack64.so: cannot open shared object file: No such file or
>> directory.
>>
>> I don't know if it is because I have a 'non-commercial' version of Intel
>> compilers (fortran and mkl), I also tried to get the 'evaluation'
>> version and I get the same behaviour.
>> Yours
>>
>> Pablo
>>
>> Chandrika escribió:
>>
>>> Dear Pablo,
>>> You need to define library paths in bashrc and ld.so.config in the etc
>>> directory (or the
>>> equivalent files for your system) and define these in site config. Also look
>>> uo the nice
>>> article by Gerhard Fecher on compiling Wien for begineers (you can download
>>> this from the Wien site).
>>> Best wishes,
>>> Chandrika
>>> ----- Original Message -----
>>> From: "Pablo de la Mora" <delamora at servidor.unam.mx>
>>> To: "A Mailing list for WIEN2k users" <wien at zeus.theochem.tuwien.ac.at>
>>> Sent: Thursday, April 26, 2007 11:02 PM
>>> Subject: Re: [Wien] Compiling for Athlon x2
>>>
>>>
>>> After compiling successfully with '-pthread' I tryed to run the program
>>> and lapw1 gives the error:
>>> [pablo at mistla prueba]$ x lapw1
>>> /home/Programas/WIEN2k/lapw1: error while loading shared libraries:
>>> libmkl_lapack64.so: cannot open shared object file: No such file or
>>> directory
>>> 0.000u 0.004s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
>>> error: command /home/Programas/WIEN2k/lapw1 lapw1.def failed
>>>
>>> I have both fortran and mkl and this library 'libmkl_lapack64.so' is in
>>> the /opt/intel... directory. I tried to copy it into the WIEN directory.
>>> without success.
>>> Thanks
>>>
>>> Pablo
>>>
>>> Pablo de la Mora escribió:
>>>
>>>
>>>> Dear Peter,
>>>> Thank you, now the code compiled OK, the options as you suggested
>>>> for an Athlon are:
>>>>
>>>> Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip
>>>> -DINTEL_VML
>>>> Linker Flags: $(FOPT) -L/opt/intel/mkl/8.0/lib/em64t
>>>> -lpthread
>>>> Preprocessor flags: '-DParallel'
>>>> R_LIB (LAPACK+BLAS): -lmkl_lapack64 -lmkl_em64t -lguide
>>>>
>>>> Current settings:
>>>> O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip
>>>> -DINTEL_VML
>>>> L Linker Flags: $(FOPT) -L/opt/intel/mkl/9.0/lib/em64t
>>>> -pthread -lpthread
>>>> P Preprocessor flags '-DParallel'
>>>> R R_LIB (LAPACK+BLAS): -lmkl_lapack64 -lmkl_em64t -lguide
>>>>
>>>> Yours
>>>> Pablo de la Mora
>>>>
>>>>
>>>> Peter Blaha escribió:
>>>>
>>>>
>>>>
>>>>> Try adding -pthread (in additon to -lpthread) to the linker-flags
>>>>>
>>>>> Pablo de la Mora schrieb:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Laurence,
>>>>>> I tried, but I don't seem to find an answer in connection to the
>>>>>> WIEN program.
>>>>>> Thanks
>>>>>> Pablo
>>>>>>
>>>>>> Laurence Marks escribió:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Google it
>>>>>>> http://www.google.com/search?q=referencia+a+%60pthread%5Fatfork%27+sin+definir&hl=en&sourceid=gd&rls=DJUS,DJUS:2006-22,DJUS:en
>>>>>>>
>>>>>>> On 4/25/07, Pablo de la Mora <delamora at servidor.unam.mx> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Dear Wien Users,
>>>>>>>> I am compiling the WIEN2k code compiling for an Athlon x2 with the
>>>>>>>> ifort 9.1.045 and mkl 9.0.018
>>>>>>>> the compiling options are:
>>>>>>>> O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip
>>>>>>>> -DINTEL_VML
>>>>>>>> L Linker Flags:
>>>>>>>> $(FOPT) -L/opt/intel/mkl/9.0/lib/em64t
>>>>>>>> -lpthread
>>>>>>>> P Preprocessor flags '-DParallel'
>>>>>>>> R R_LIB (LAPACK+BLAS): -lmkl_lapack64 -lmkl_em64t -lguide
>>>>>>>> and I get
>>>>>>>> SRC_aim/compile.msg:/opt/intel/mkl/9.0/lib/em64t/libguide.so:
>>>>>>>> referencia
>>>>>>>> a `pthread_atfork' sin definir
>>>>>>>> in other words; undefined reference to `pthread_atfork'
>>>>>>>> This reference appears in:
>>>>>>>> aim, filtvec, lapw1, lapw2, lapw7, lapwdm, lapwso, min,
>>>>>>>> pairhess, qtl and structeditor
>>>>>>>> as a consequence this gives an error and these programs are not
>>>>>>>> compiled.
>>>>>>>>
>>>>>>>> Does anyone have any suggestions.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Pablo
>>>>>>>> _______________________________________________
>>>>>>>> Wien mailing list
>>>>>>>> Wien at zeus.theochem.tuwien.ac.at
>>>>>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
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