[gmx-users] question

Mon May 18 22:08:01 CEST 2015

On Mon, May 18, 2015 at 9:15 PM Andrew Bostick <andrew.bostick1 at gmail.com>
wrote:

> Dear Mark
>
> I installed the newest version of cmake (3.2.2).
>
> After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
> CUDA_TOOLKIT_ROOT_DIR not found or specified
> -- Could NOT find CUDA (missing:  CUDA_TOOLKIT_ROOT_DIR
> CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at
> least version "4.0")
> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> acceleration
> -- The GROMACS-managed build of FFTW 3 will configure with the following
> optimizations: --enable-sse2
> Downloading:
> http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz
> -- [download 100% complete]
> CMake Error at tests/CMakeLists.txt:57 (message):
>   error: downloading
>   'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed
>
>   status_code: 1
>
>   status_string: "Unsupported protocol"
>
>   log: Hostname was NOT found in DNS cache
>
>     Trying 130.237.25.133...
>
>   Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0)
>
>   GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1
>
>   User-Agent: curl/7.38.0
>
>   Host: gerrit.gromacs.org
>
>   Accept: */*
>
>
>
>   HTTP/1.1 302 Found
>
>   Date: Mon, 18 May 2015 19:11:21 GMT
>
>   Server Apache/2.2.22 (Ubuntu) is not blacklisted
>
>   Server: Apache/2.2.22 (Ubuntu)
>
>   Location:
>   https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
>
>   Vary: Accept-Encoding
>
>   Content-Length: 337
>
>   Content-Type: text/html; charset=iso-8859-1
>
>
>
>   Ignoring the response-body
>
>   <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
>
>   <html><head>
>
>   <title>302 Found</title>
>
>   </head><body>
>
>   <h1>Found</h1>
>
>   <p>The document has moved <a
>   href="
> https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz
> ">here</a>.</p>
>
>
>   <hr>
>
>   <address>Apache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port
>   80</address>
>
>   </body></html>
>
>   Connection #0 to host gerrit.gromacs.org left intact
>
>   Issue another request to this URL:
>   'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz'
>
>   Protocol "https" not supported or disabled in libcurl
>

All of the above redirection is correct behaviour for our setup, but the
problem is that your CMake is linking to an unsuitable version of libcurl.
See http://www.cmake.org/pipermail/cmake-developers/2013-July/019430.html
for background. You can maybe change your openssl library, file a bug with
Ubuntu, use a Kitware-provided CMake binary, build your own, download the
GROMACS tests yourself...

Mark

>   Closing connection -1
>
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeOutput.log".
> See also
> "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeError.log".
>
> ---------------------------------------------------------
>
> the content of CMakeOutput.log file is as follows:
>
> The system is: Linux - 2.6.32-431.11.2.el6.x86_64 - x86_64
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> succeeded.
> Compiler: /usr/bin/cc
> Build flags:
> Id flags:
>
> The output was:
> 0
>
>
> Compilation of the C compiler identification source "CMakeCCompilerId.c"
> produced "a.out"
>
> The C compiler identification is GNU, found in
>
> "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdC/a.out"
>
> Compiling the CXX compiler identification source file
> "CMakeCXXCompilerId.cpp" succeeded.
> Compiler: /usr/bin/c++
> Build flags:
> Id flags:
>
> The output was:
> 0
>
>
> Compilation of the CXX compiler identification source
> "CMakeCXXCompilerId.cpp" produced "a.out"
>
> The CXX compiler identification is GNU, found in
>
> "/export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/3.2.2/CompilerIdCXX/a.out"
>
> Determining if the C compiler works passed with the following output:
> Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
>
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2875484959/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2875484959.dir/build.make
> CMakeFiles/cmTryCompileExec2875484959.dir/build
> @
> "CMakeOutput.log" 1317L, 113885C
>
> ----------------------------------------------------------
> the content of CMakeError.log file is as follows:
>
> Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following
> output:
> Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
>
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2440156335/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2440156335.dir/build.make
> CMakeFiles/cmTryCompileExec2440156335.dir/build
> gmake[1]: Entering directory
> `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp'
> /usr/local/bin/cmake -E cmake_progress_report
> /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/CMakeFiles 1
> Building C object CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o
> /usr/bin/cc   -DCFLAGS_EXCESS_PREC -fexcess-precision=fast   -o
> CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o   -c
> /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/src.c
> cc1: error: unrecognized command line option "-fexcess-precision=fast"
> gmake[1]: *** [CMakeFiles/cmTryCompileExec2440156335.dir/src.c.o] Error 1
> gmake[1]: Leaving directory
> `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec2440156335/fast] Error 2
>
> Source file was:
> int main(void) { return 0; }
> Performing C++ SOURCE FILE Test CXXFLAGS_EXCESS_PREC failed with the
> following output:
> Change Dir: /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp
>
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec188469838/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec188469838.dir/build.make
> CMakeFiles/cmTryCompileExec188469838.dir/build
> gmake[1]: Entering directory
> `/state/partition1/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp'
> /usr/local/bin/cmake -E cmake_progress_report
> /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/CMakeFiles 1
> Building CXX object CMakeFiles/cmTryCompileExec188469838.dir/src.cxx.o
> /usr/bin/c++    -DCXXFLAGS_EXCESS_PREC -fexcess-precision=fast   -o
> CMakeFiles/cmTryCompileExec188469838.dir/src.cxx.o -c
> /export/apps/gromacs/gromacs-5.0.5/build/CMakeFiles/CMakeTmp/src.cxx
> cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
> ---------------------------------------------------------
>
> How to resolve this issue?
> Thanks in advance
> --
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