Unable to install VOTCA-CSG

[Yuta-Yoshimoto]

Dear all,

I haven't been able to install VOTCA-CSG.
According to the error message below, it seems like gsl_linalg_QR_decomp was not found in /usr/local/lib/libgsl.so.
Then, the system failed to find mkl_boost_ublas_matrix_prod.hpp, too.
However, I confirmed via 'strings' that gsl_linalg_QR_decomp was actually included in /usr/local/lib/libgsl.so.
What should I do to handle this issue?
I would appreciate it if you would give me some comments on this issue.

--2017-05-02 19:51:07--  https://raw.githubusercontent.com/votca/buildutil/master/build.sh
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2017-05-02 19:51:08 (10.8 MB/s) - “build.sh” saved [31549/31549]

This is VOTCA build.sh, version 2.1.3
Install prefix is '/home/yyoshimoto/votca'
Using 17 jobs for make/ninja
Working on tools
Download tarball votca-tools-1.4.tar.gz from https://github.com/votca/tools/archive/v1.4.tar.gz
--2017-05-02 19:51:08--  https://github.com/votca/tools/archive/v1.4.tar.gz
Resolving github.com... 192.30.255.113, 192.30.255.112
Connecting to github.com|192.30.255.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/votca/tools/tar.gz/v1.4 [following]
--2017-05-02 19:51:08--  https://codeload.github.com/votca/tools/tar.gz/v1.4
Resolving codeload.github.com... 192.30.253.120, 192.30.253.121
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cmake -DCMAKE_INSTALL_PREFIX='/home/yyoshimoto/votca'  -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.41.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") 
-- checking for module 'gsl'
--   found gsl, version 2.3
-- Found GSL: /usr/local/lib/libgsl.so  
-- Looking for gsl_linalg_QR_decomp in /usr/local/lib/libgsl.so;
-- Looking for gsl_linalg_QR_decomp in /usr/local/lib/libgsl.so; - not found
-- Found GSLCBLAS: /usr/local/lib/libgslcblas.so  
-- Looking for cblas_dsyrk in /usr/local/lib/libgslcblas.so;
-- Looking for cblas_dsyrk in /usr/local/lib/libgslcblas.so; - found
-- Looking for gsl_linalg_QR_lssolve in /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so;
-- Looking for gsl_linalg_QR_lssolve in /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so; - found
-- Intel(R) MKL was found:
  MKL_INCLUDE_DIRS: /opt/intel/composer_xe_2015.2.164/mkl/include
  MKL_LIBRARY_DIRS: /opt/intel/composer_xe_2015.2.164/mkl/lib/intel64;/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64
  MKL_LIBRARIES: /opt/intel/composer_xe_2015.2.164/mkl/lib/intel64/libmkl_rt.so;/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64/libiomp5.so;/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64/libimf.so
-- MKL found, overloading uBLAS prod()
-- checking for module 'fftw3'
--   found fftw3, version 3.3.6-pl2
-- Found FFTW3: /usr/local/lib/libfftw3.so  
-- Looking for fftw_plan_r2r_1d in /usr/local/lib/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in /usr/local/lib/libfftw3.so; - found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
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-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
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-- Looking for C++ include list
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-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- checking for module 'expat'
--   found expat, version 2.2.0
-- Found EXPAT: /usr/local/lib/libexpat.so  
-- checking for module 'sqlite3'
--   found sqlite3, version 3.18.0
-- Found SQLITE3: /usr/local/lib/libsqlite3.so  
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Found Doxygen: /usr/local/bin/doxygen (found version "1.8.13") 
-- 
-- The following OPTIONAL packages have been found:

 * GSL
 * MKL
 * FFTW3
 * EXPAT
 * PkgConfig
 * SQLITE3
 * Doxygen

-- The following REQUIRED packages have been found:

 * Threads
 * Boost (required version >= 1.39.0)

-- Configuring done
-- Generating done
-- Build files have been written to: /home/yyoshimoto/votca/src/tools
cleaning tools
buidling tools
Scanning dependencies of target intel
Scanning dependencies of target votca_tools_manpages
Scanning dependencies of target gitversion
[  2%] [  2%] Built target votca_tools_manpages
Creating directories for 'intel'
[  2%] Built target gitversion
Scanning dependencies of target votca_tools
[  4%] [  6%] [  9%] [ 11%] [ 13%] [ 16%] [ 18%] [ 20%] [ 23%] [ 30%] [ 32%] [ 32%] [ 32%] [ 34%] [ 37%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
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Performing download step (download, verify and extract) for 'intel'
[ 44%] [ 46%] [ 48%] -- downloading...
     src='http://software.intel.com/sites/default/files/managed/76/8c/intel-mkl-and-boost-example.zip'
     dst='/home/yyoshimoto/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip'
     timeout='none'
Building CXX object src/libtools/CMakeFiles/votca_tools.dir/parsexml.cc.o
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[ 51%] In file included from /home/yyoshimoto/votca/src/tools/src/libtools/cubicspline.cc:22:
/home/yyoshimoto/votca/src/tools/include/votca/tools/linalg.h:24:47: error: mkl_boost_ublas_matrix_prod.hpp: No such file or directory
In file included from /home/yyoshimoto/votca/src/tools/src/libtools/akimaspline.cc:22:
/home/yyoshimoto/votca/src/tools/include/votca/tools/linalg.h:24:47: error: mkl_boost_ublas_matrix_prod.hpp: No such file or directory
In file included from /home/yyoshimoto/votca/src/tools/src/libtools/linspline.cc:22:
/home/yyoshimoto/votca/src/tools/include/votca/tools/linalg.h:24:47: error: mkl_boost_ublas_matrix_prod.hpp: No such file or directory
Building CXX object src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
[ 53%] [ 55%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o
-- [download 77% complete]
-- [download 100% complete]
-- downloading... done
[ 58%] [ 60%] -- verifying file...
     file='/home/yyoshimoto/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip'
-- verifying file... done
Building CXX object src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o
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-- extracting...
     src='/home/yyoshimoto/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip'
     dst='/home/yyoshimoto/votca/src/tools/intel/src/intel'
-- extracting... [tar xfz]
In file included from /home/yyoshimoto/votca/src/tools/src/libtools/linalg.cc:17:
/home/yyoshimoto/votca/src/tools/include/votca/tools/linalg.h:24:47: error: mkl_boost_ublas_matrix_prod.hpp: No such file or directory
-- extracting... [analysis]
-- extracting... [rename]
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[ 69%] [ 72%] [ 74%] No patch step for 'intel'
No update step for 'intel'
Building CXX object src/libtools/CMakeFiles/votca_tools.dir/statement.cc.o
[ 76%] make[2]: *** [src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 79%] make[2]: *** [src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o] Error 1
[ 81%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/cholesky.cc.o
[ 83%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/qrsolve.cc.o
No configure step for 'intel'
Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/svd.cc.o
[ 86%] No build step for 'intel'
/home/yyoshimoto/votca/src/tools/src/libtools/linalg.cc: In function ‘double votca::tools::linalg_traceofProd(const boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, const boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&)’:
/home/yyoshimoto/votca/src/tools/src/libtools/linalg.cc:169: error: invalid initialization of reference of type ‘const boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&’ from expression of type ‘const boost::numeric::ublas::unbounded_array<double, std::allocator<double> >’
/home/yyoshimoto/votca/src/tools/src/libtools/linalg.cc:170: error: invalid initialization of reference of type ‘const boost::numeric::ublas::vector<double, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&’ from expression of type ‘const boost::numeric::ublas::unbounded_array<double, std::allocator<double> >’
[ 88%] No install step for 'intel'
make[2]: *** [src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o] Error 1
make[2]: *** [src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o] Error 1
[ 90%] Completed 'intel'
[ 90%] Built target intel
make[1]: *** [src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
make: *** [all] Error 2

Best,
Yuta

Yoshimoto, Yuta, Ph.D.
Department of Mechanical Engineering,
The University of Tokyo
Tel: +81-3-5841-1897
Email: yyoshimoto@fel.t.u-tokyo.ac.jp

[junghans]

According to the error message below, it seems like gsl_linalg_QR_decomp was not found in /usr/local/lib/libgsl.so. However, I confirmed via 'strings' that gsl_linalg_QR_decomp was actually included in /usr/local/lib/libgsl.so.

No worries, it is just a test. Later, cmake found gsl_linalg_QR_lssolve in /usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so, meaning on your OS gsl needs to be linked against libgsl.so and ibgslcblas.so.

Then, the system failed to find mkl_boost_ublas_matrix_prod.hpp, too. What should I do to handle this issue?

@JensWehner can help with that issue, but for now try to disabling MKL by adding -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON to command line of build.sh. MKL isn't used in VOTCA-CSG, but only VOTCA-CTP, so it won't hurt much.

[junghans]

And can you please check first if the problem persists in the development version: https://github.com/votca/csg/wiki/Installing#development-version

[JensWehner]

My guess is, it is still the race condition. I have not yet found a way to force to the the download of the header files before the rest of the stuff. According to the log file this is exactly what happened. Maybe default should be mkl off. Cheers Jens 2017-05-02 17:18 GMT+02:00 Christoph Junghans <notifications@github.com>:

…

And can you please check first if the problem persists in the development version: https://github.com/votca/csg/wiki/Installing#development-version — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#209 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALk6aWfPCQhAadOjcEJ3LvxpVdO2FhKTks5r10k5gaJpZM4NOANQ> .

[junghans]

Actually we fixed that in votca/tools@99b8bc5, but that patch is not part of v1.4.

Time for v1.4.1 ?

[junghans]

@Yuta-Yoshimoto is it working for you now?

[Yuta-Yoshimoto]

Dear Christoph and Jens,

Thank you so much for your kind comments, and sorry for my late reply.

Unfortunately, I was not able to install the latest version of VOTCA-CSG by adding -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON (see the attachment 'error01.txt').
Also, I couldn't install the development version (error02.txt), even by adding the above option (error03.txt).
There is a chance that the Boost libraries have something to do with this issue.

error01.txt
error02.txt
error03.txt

Best,
Yuta

[Yuta-Yoshimoto]

Dear Christoph and Jens,

I installed the latest version of the Boost libraries Ver. 1.64.0, but there are still some errors saying ‘make_array’ is not a member of ‘boost::serialization’ (error.04.txt).
Alas...

error04.txt

Best,
Yuta

[JensWehner]

Hello Yuta, could you do it once more with boost 1.58? Boost before 1.48 apparently is a bit fishy and the newest boost versions have problems with serialisation. On that we have to work. Cheers Jens 2017-05-11 12:25 GMT+02:00 Yuta Yoshimoto <notifications@github.com>:

…

Dear Christoph and Jens, I installed the latest version of the Boost libraries Ver. 1.64.0, but there are still some errors saying ‘make_array’ is not a member of ‘boost::serialization’ (error.04.txt). Alas... error04.txt <https://github.com/votca/csg/files/992653/error04.txt> Best, Yuta — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#209 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALk6aa-lpT25Sy-L6jdWTh-B4Y4pODzgks5r4uIzgaJpZM4NOANQ> .

[Yuta-Yoshimoto]

Hi Jens,

Thanks to your suggestion, I was able to install VOTCA-CSG using Boost 1.58.0.
However, I had the following error message when I tried to install it using g++ compiler.
It looks like g++ compiler of my workstation is old, and doesn't include C++11 compiler.
So, I used icc 15.0.2 compiler, and was succeccful in installing VOTCA-CSG!
I hope it'll go well...

cmake -DCMAKE_INSTALL_PREFIX='/home/yyoshimoto/votca' -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Failed
CMake Error at CMakeLists.txt:35 (message):
Could not find a C++-11 compiler

-- Configuring incomplete, errors occurred!
See also "/home/yyoshimoto/votca/src/csg/CMakeFiles/CMakeOutput.log".
See also "/home/yyoshimoto/votca/src/csg/CMakeFiles/CMakeError.log".

Best,
Yuta

[junghans]

First of all, boost-1.64 is broken and this error has nothing to do with VOTCA, see here.

Besides a reasonable boost (1.58 is ok) you need a c++-11 compiler, so at least gcc-4.8, I think.

As an alternative, VOTCA comes with Fedora and OpenSuse, so you can just install it using dnf/zypper.

[Yuta-Yoshimoto]

Dear Christoph and Jens,

I tried csg-tutorials/spce/ibi, but I couldn't run the simulation.
The error message is as follows:

ERROR:

run_gromacs.sh: grompp binary 'gmx' not found

For details see the logfile /home/yyoshimoto/Desktop/ibi/spce/ibi/inverse.log

I already installed the double-presicion version of GROMACS with the binary file 'gmx_d'.
Should I install the single-precision version?

Best,
Yuta

[schererc]

You have to change the inverse.gromacs.grompp.bin setting in the settings.xml file to the name/path of the binary (gmx_d grompp) and also the inverse.gromacs.mdrun.command setting to gmx_d mdrun, as the defaults are gmx grompp and gmx mdrun.

Best

Christoph

[Yuta-Yoshimoto]

Hi Christoph,

Thank you so much for your comment.
I was able to run the IBI simulation of SPC/E water!

By the way, is it possible to output tablated 'mean force' as well as CG-CG.pot.new?
If it's not possible, I'm alright since I can evaluate the mean force from the tablated PMF.

Best,
Yuta

[junghans]

Good to hear!

For the mean force, just look into step_000 the initial guess for the potential is the potential of mean force.