Thank you. I found related contents in sec 5.5.5. I understand it now. <br><br><br><br><div class="gmail_quote">On Fri, Feb 22, 2013 at 3:05 PM, Peter Blaha <span dir="ltr"><<a href="mailto:pblaha@theochem.tuwien.ac.at" target="_blank">pblaha@theochem.tuwien.ac.at</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">No. Please read the UG about parallelization. k-point parallelization is done via scripts.<br>
<br>
Am 22.02.2013 20:28, schrieb Long Zhang:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thank you for the information.<br>
I think I had wrong idea about k-point parallel. If it doesn't use<br>
OpenMP then it's perfectly fine for me. I'll drop the idea of<br>
finegrained parallel in this installation.<br>
<br>
Just want to confirm, for using k-point parallel only, MPICH2 is still<br>
required, is that right?<br>
<br>
Thanks.<br>
Long<br>
<br>
<br>
<br>
<br>
On Fri, Feb 22, 2013 at 11:04 AM, Laurence Marks<br></div><div class="im">
<<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a> <mailto:<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.<u></u>edu</a>>> wrote:<br>
<br>
As Peter said, the simplest approach is just k-point parallel which<br>
does not need OpenMP. The rate limiting steps are lapack calls which<br>
the Intel mkl is good for.<br>
<br>
Whether mpi is good for a small cluster such as you have in not so<br>
clear. Peter has benchmarked the mpi version and his conclusion is<br>
that it is not useful; I have benchmarked on my cluster and I have<br>
consistently found the mpi versions to be faster than the Intel<br>
threading. I suspect that it really depends upon many details specific<br>
to the systems, for instance cross-core optimizations, network and<br>
memory speed....<br>
<br>
Not a complete answer, but for certain the simplest approach is to<br>
just use k-point parallel.<br>
<br>
On Fri, Feb 22, 2013 at 9:55 AM, Long Zhang <<a href="mailto:lzhang6789@gmail.com" target="_blank">lzhang6789@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:lzhang6789@gmail.com" target="_blank">lzhang6789@gmail.com</a>>> wrote:<br>
><br>
> That's true I agree. If the k-point parallel version does not<br>
need mpi, then<br>
> it's OpenMP I suppose (please correct me if it's not). But I<br>
really don't<br>
> want to run OpenMP because it will mess my other applications up.<br>
><br>
> I am building it on a small server of 2 Opteron 12-core cpus.<br>
It's just a<br>
> dual-cpu system, not a cluster. I am not sure if I can gain<br>
enough speed-up<br>
> by using 24 cores. Anyway if I want a little k-point parallel,<br>
can I choice<br>
> to use mpi? or there is no such choice at all?<br>
><br>
> Thank you very much.<br>
> Long<br>
><br>
><br>
> On Fri, Feb 22, 2013 at 3:07 AM, Peter Blaha<br></div>
<<a href="mailto:pblaha@theochem.tuwien.ac.at" target="_blank">pblaha@theochem.tuwien.ac.at</a> <mailto:<a href="mailto:pblaha@theochem.tuwien.ac.at" target="_blank">pblaha@theochem.<u></u>tuwien.ac.at</a>>><div>
<div class="h5"><br>
> wrote:<br>
>><br>
>> I keep saying this all the time:<br>
>><br>
>> The mpi-parallel version needs special hardware !<br>
>><br>
>> It is not of much use on a single quadcore-cpu.<br>
>> A cluster needs a fast network like infiniband.<br>
>><br>
>> Only then the installation of the mpi-version make sense.<br>
>><br>
>> We have a k-point parallel version, which does not need mpi, but is<br>
>> perfect for a small cluster with a common NFS filesystem.<br>
>><br>
>><br>
>> Am 22.02.2013 06:20, schrieb Long Zhang:<br>
>>><br>
>>><br>
>>> Hello,<br>
>>><br>
>>> I am trying to install the current version 12.1 on Ubuntu 12.04<br>
>>> (64-bit). I met some problem related to mpi, can someone please<br>
give me<br>
>>> some hint? Thanks in advance.<br>
>>><br>
>>> The situation is like this, on a freshly installed Ubuntu 12.04<br>
64bit, I<br>
>>> installed current version Intel Fortran Composer XE 2013.2.146, and<br>
>>> installed MPICH2 and FFTW3 via Ubuntu Software Center.<br>
>>><br>
>>> Before run the siteconfig_lapw, I checked<br>
>>> which ifort<br>
>>> /opt/intel/composer_xe_2013.2.<u></u>146/bin/intel64/ifort<br>
>>> which mpif90<br>
>>> /usr/bin/mpif90<br>
>>><br>
>>> and did the following 3 lines in the terminal<br>
>>> source /opt/intel/composer_xe_2013.2.<u></u>146/bin/compilervars.sh<br>
intel64<br>
>>> export<br>
>>><br>
>>><br>
LD_LIBRARY_PATH=$LD_LIBRARY_<u></u>PATH:/opt/intel/composer_xe_<u></u>2013.2.146/mkl/lib/intel64<br>
>>> export MKLROOT=/opt/intel/composer_<u></u>xe_2013.2.146/mkl/<br>
>>><br>
>>> Then I run the siteconfig_lapw, and selected system as<br>
"ifort12+mkl"<br>
>>> (the first one), selected compilers as "ifort" and "cc", selected<br>
>>> "finegrained parallel" and "mpif90", and got error message like<br>
this:<br>
>>><br>
>>> ------------------------------<u></u>----------------- cut1<br>
>>> ------------------------------<u></u>-----------------<br>
>>> Compile time errors (if any) were:<br>
>>> SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_hf/compile.msg:make: *** [rp] Error 2<br>
>>> SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_hf/compile.msg:make: *** [cp] Error 2<br>
>>> SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_lapw0/compile.msg:make: *** [para] Error 2<br>
>>> SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_lapw1/compile.msg:make: *** [rp] Error 2<br>
>>> SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_lapw1/compile.msg:make: *** [cp] Error 2<br>
>>> SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_lapw2/compile.msg:make: *** [rp] Error 2<br>
>>> SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1<br>
>>> SRC_lapw2/compile.msg:make: *** [cp] Error 2<br>
>>> ------------------------------<u></u>----------------- cut1<br>
>>> ------------------------------<u></u>-----------------<br>
>>><br>
>>> I looked into SRC_lapw1/compile.msg, and the detailed error is:<br>
>>><br>
>>> ------------------------------<u></u>----------------- cut2<br>
>>> ------------------------------<u></u>-----------------<br>
>>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3<br>
>>> -traceback -DParallel -c modules_tmp_.F<br>
>>><br>
>>><br>
------------------------------<u></u>------------------------------<u></u>--------------<br>
>>> The Open MPI wrapper compiler was unable to find the specified<br>
compiler<br>
>>> gfortran in your PATH.<br>
>>><br>
>>> Note that this compiler was either specified at configure time<br>
or in<br>
>>> one of several possible environment variables.<br>
>>><br>
>>><br>
------------------------------<u></u>------------------------------<u></u>--------------<br>
>>> make[1]: *** [modules.o] Error 1<br>
>>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_<u></u>lapw1'<br>
>>> make: *** [rp] Error 2<br>
>>> ------------------------------<u></u>----------------- cut2<br>
>>> ------------------------------<u></u>-----------------<br>
>>><br>
>>> It seems OpenMPI was invoked and it looked for gfortran. I<br>
don't have<br>
>>> gfortran installed at all, but I found I have openmpi<br>
installed. I then<br>
>>> used Ubuntu Software Center to search openmpi and uninstalled<br>
related<br>
>>> packages. I restarted the system and repeated the siteconfig_lapw.<br>
>>> However I still get error message, not same but similar, it<br>
still looks<br>
>>> for gfortran, for examplethe SRC_lapw1/compile.msg shows:<br>
>>><br>
>>><br>
>>> ------------------------------<u></u>----------------- cut3<br>
>>> ------------------------------<u></u>-----------------<br>
>>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3<br>
>>> -traceback -DParallel -c modules_tmp_.F<br>
>>> /usr/bin/mpif90: line 370: gfortran: command not found<br>
>>> make[1]: *** [modules.o] Error 127<br>
>>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_<u></u>lapw1'<br>
>>> make: *** [rp] Error 2<br>
>>> ------------------------------<u></u>----------------- cut3<br>
>>> ------------------------------<u></u>-----------------<br>
>>><br>
>>> I did not specify to use gfortran anywhere in the setupof<br>
>>> siteconfig_lapw, I don't see why mpif90 keeps looking for it.<br>
How can I<br>
>>> fix this problem? Thanks a lot.<br>
>>><br>
>>> Regards,<br>
>>> Long Zhang<br>
>>><br>
>>><br>
>>> ______________________________<u></u>_________________<br>
>>> Wien mailing list<br>
>>> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.<u></u>at</a><br></div></div>
<mailto:<a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.<u></u>tuwien.ac.at</a>><div class="im"><br>
>>> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.<u></u>ac.at/mailman/listinfo/wien</a><br>
>>><br>
>><br>
>> --<br>
>> Peter Blaha<br>
>> Inst.Materials Chemistry<br>
>> TU Vienna<br>
>> Getreidemarkt 9<br>
>> A-1060 Vienna<br>
>> Austria<br></div>
>> <a href="tel:%2B43-1-5880115671" value="+4315880115671" target="_blank">+43-1-5880115671</a> <tel:%2B43-1-5880115671><div class="im"><br>
>><br>
>> ______________________________<u></u>_________________<br>
>> Wien mailing list<br>
>> <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.<u></u>at</a><br></div>
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>> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.<u></u>ac.at/mailman/listinfo/wien</a><br>
><br>
><br>
<br>
<br>
<br>
--<br>
Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br></div>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> <<a href="http://www.numis.northwestern.edu" target="_blank">http://www.numis.<u></u>northwestern.edu</a>><br>
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"Research is to see what everybody else has seen, and to think what<br>
nobody else has thought"<br>
Albert Szent-Gyorgi<br>
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<br>
</div></blockquote><div class="HOEnZb"><div class="h5">
<br>
-- <br>
Peter Blaha<br>
Inst.Materials Chemistry<br>
TU Vienna<br>
Getreidemarkt 9<br>
A-1060 Vienna<br>
Austria<br>
<a href="tel:%2B43-1-5880115671" value="+4315880115671" target="_blank">+43-1-5880115671</a><br>
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</div></div></blockquote></div><br>