CMake error during build, and solution

[Robert Elder]

Hi Users:

I just wanted to share a Votca compilation problem and solution I encountered recently. When running the build.sh script, as described here (https://github.com/votca/csg/wiki/Installing#from-source), I encountered this error:

[snip]

cleaning tools
buidling tools
Scanning dependencies of target votca_tools_manpages
[  0%] Built target votca_tools_manpages
Scanning dependencies of target intel
Scanning dependencies of target gitversion
Current git revision is 7ca4a6d
[  0%] Built target gitversion
Scanning dependencies of target votca_tools
[  2%] Creating directories for 'intel'
[  4%] Performing download step (download, verify and extract) for 'intel'
[  7%] -- downloading...
     src='http://software.intel.com/sites/default/files/managed/76/8c/intel-mkl-and-boost-example.zip'
     dst='/p/home/elderr/src/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip'
     timeout='none'
[  9%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
CMake Error at intel-stamp/download-intel.cmake:9 (file):
  file DOWNLOAD HASH mismatch

    for file: [/p/home/elderr/src/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip]
      expected hash: [b957ee63a2167ad21b650b47726cd55c]
        actual hash: [d41d8cd98f00b204e9800998ecf8427e]



make[2]: *** [intel/src/intel-stamp/intel-download] Error 1
make[1]: *** [CMakeFiles/intel.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

[snip]

Basically CMake failed because the hashes on intel-mkl-and-boost-example.zip did not match -- the reason being that the downloaded intel-mkl-and-boost-example.zip was a zero byte file! I have no idea why; perhaps some obscure problem on our machine. I don't know CMake well enough, but it seems to be running with multiple threads -- maybe a race condition on download vs. hash? Just speculation.

Anyway I solved this by downloading the 'src' file from http://software.intel.com manually and putting it in the required location ('dst'). Then I reran the build script, it picked up where it left off and completed without a problem.

Hopefully that helps someone. Thanks for this great tool!
-Robert Elder

[Christoph Junghans]

Hi Robert,

thanks for reporting, I turned it into a issue of github:
https://github.com/votca/tools/issues/8

On a side note, mkl is only needed if you are planning to build
votca-ctp, votca-csg isn't really using it.

Christoph

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Christoph Junghans
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[jensw...@gmail.com]

Hi Robert,

I was unable to reproduce the error. May you send me the complete build log?

Cheers

Jens

[Robert Elder]

The machine I was using to build is down at the moment, but I'll send a build log when I can.

Cheers,
Robert

[Robert Elder]

Hi Jens and list:

I have attached the scripts I used to build VOTCA, and the resulting log files. I called the scripts like `source build.intel.sh &> log.build.intel`. The build fails without the options to disable Intel MKL, the 'intel' files, with either 1 process (./build.sh -j1) or many processes (e.g. ./build.sh -j12, or without -j option). The build succeeds with the options to disable Intel MKL (-DWITH_MKL=OFF -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON), the 'no-intel' files, again regardless of how many processes.

When I reported the problem it was the 1.4 release, but now it looks like it's 1.5-dev. This is on one of our HPC clusters, an SGI ICE X machine.

Let me know if I can provide any other information.

Cheers,
Robert

[Christoph Junghans]

Hi Robert,

2017-01-25 9:16 GMT-07:00 Robert Elder <rme...@gmail.com>:
> Hi Jens and list:
>
> I have attached the scripts I used to build VOTCA, and the resulting log
> files. I called the scripts like `source build.intel.sh &> log.build.intel`.
> The build fails without the options to disable Intel MKL, the 'intel' files,
> with either 1 process (./build.sh -j1) or many processes (e.g. ./build.sh
> -j12, or without -j option). The build succeeds with the options to disable
> Intel MKL (-DWITH_MKL=OFF -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON), the
> 'no-intel' files, again regardless of how many processes.
>
> When I reported the problem it was the 1.4 release, but now it looks like
> it's 1.5-dev. This is on one of our HPC clusters, an SGI ICE X machine.
>
> Let me know if I can provide any other information.

The later build error is a missing dependency, which I fixed
<https://github.com/votca/tools/commit/99b8bc547a76b2afaf97d45149a8a756b5c8e775>
however one out of 10 times I get an download error (with the same
mismatching hash!) as well, so I am guess it is a problem with intel
web server.

Christoph

[Christoph Junghans]

Robert,

do you still have the intel zip with the hash
d41d8cd98f00b204e9800998ecf8427e (use md5sum)?

Christoph

[Robert Elder]

I already deleted it, but it was a zero-byte file. I get the same hash if I do: touch tmpfile; md5sum tmpfile

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>
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> Christoph Junghans
> Web: http://www.compphys.de



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Christoph Junghans
Web: http://www.compphys.de

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[Christoph Junghans]

2017-01-25 11:03 GMT-07:00 Robert Elder <rme...@gmail.com>:
> I already deleted it, but it was a zero-byte file. I get the same hash if I
> do: touch tmpfile; md5sum tmpfile

Yeah, google told me the same thing ;-)
So this issue seems to be a bug in cmake or intel webserver.

Christoph

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