Thank you for the information. <br>I think I had wrong idea about k-point parallel. If it doesn't use OpenMP then it's perfectly fine for me. I'll drop the idea of finegrained parallel in this installation. <br>
<br>Just want to confirm, for using k-point parallel only, MPICH2 is still required, is that right? <br><br>Thanks.<br>Long <br><br> <br><br><br><div class="gmail_quote">On Fri, Feb 22, 2013 at 11:04 AM, Laurence Marks <span dir="ltr"><<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<div class="im HOEnZb"><br>
On Fri, Feb 22, 2013 at 9:55 AM, Long Zhang <<a href="mailto:lzhang6789@gmail.com">lzhang6789@gmail.com</a>> wrote:<br>
><br>
> That's true I agree. If the k-point parallel version does not need mpi, then<br>
> it's OpenMP I suppose (please correct me if it's not). But I 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. It's just a<br>
> dual-cpu system, not a cluster. I am not sure if I can gain enough speed-up<br>
> by using 24 cores. Anyway if I want a little k-point parallel, 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 <<a href="mailto:pblaha@theochem.tuwien.ac.at">pblaha@theochem.tuwien.ac.at</a>><br>
> wrote:<br>
>><br>
</div><div class="HOEnZb"><div class="h5">>> 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 give me<br>
>>> some hint? Thanks in advance.<br>
>>><br>
>>> The situation is like this, on a freshly installed Ubuntu 12.04 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_2013.2.146/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_2013.2.146/bin/compilervars.sh intel64<br>
>>> export<br>
>>><br>
>>> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64<br>
>>> export MKLROOT=/opt/intel/composer_xe_2013.2.146/mkl/<br>
>>><br>
>>> Then I run the siteconfig_lapw, and selected system as "ifort12+mkl"<br>
>>> (the first one), selected compilers as "ifort" and "cc", selected<br>
>>> "finegrained parallel" and "mpif90", and got error message like this:<br>
>>><br>
>>> ----------------------------------------------- cut1<br>
>>> -----------------------------------------------<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>
>>> ----------------------------------------------- cut1<br>
>>> -----------------------------------------------<br>
>>><br>
>>> I looked into SRC_lapw1/compile.msg, and the detailed error is:<br>
>>><br>
>>> ----------------------------------------------- cut2<br>
>>> -----------------------------------------------<br>
>>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3<br>
>>> -traceback -DParallel -c modules_tmp_.F<br>
>>><br>
>>> --------------------------------------------------------------------------<br>
>>> The Open MPI wrapper compiler was unable to find the specified compiler<br>
>>> gfortran in your PATH.<br>
>>><br>
>>> Note that this compiler was either specified at configure time or in<br>
>>> one of several possible environment variables.<br>
>>><br>
>>> --------------------------------------------------------------------------<br>
>>> make[1]: *** [modules.o] Error 1<br>
>>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1'<br>
>>> make: *** [rp] Error 2<br>
>>> ----------------------------------------------- cut2<br>
>>> -----------------------------------------------<br>
>>><br>
>>> It seems OpenMPI was invoked and it looked for gfortran. I don't have<br>
>>> gfortran installed at all, but I found I have openmpi installed. I then<br>
>>> used Ubuntu Software Center to search openmpi and uninstalled related<br>
>>> packages. I restarted the system and repeated the siteconfig_lapw.<br>
>>> However I still get error message, not same but similar, it still looks<br>
>>> for gfortran, for examplethe SRC_lapw1/compile.msg shows:<br>
>>><br>
>>><br>
>>> ----------------------------------------------- cut3<br>
>>> -----------------------------------------------<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_lapw1'<br>
>>> make: *** [rp] Error 2<br>
>>> ----------------------------------------------- cut3<br>
>>> -----------------------------------------------<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. How can I<br>
>>> fix this problem? Thanks a lot.<br>
>>><br>
>>> Regards,<br>
>>> Long Zhang<br>
>>><br>
>>><br>
>>> _______________________________________________<br>
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>>><br>
>><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">+43-1-5880115671</a><br>
>><br>
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><br>
><br>
<br>
<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a> <a href="tel:1-847-491-3996" value="+18474913996">1-847-491-3996</a><br>
"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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