Installation problem: Boost specification
I can not find in the documentation how to specify the Boost library. 1. I’ve unzipped the tar.bz2 file in the ThirdParty directory, but nektar still tries to download the tar.bz2 file. 2. I have a boost 1.59 installed, and the bin directory is in the LD_LIBRARY_PATH but the installation is not finding or using it. Victor.
Hi Victor, Assuming you have the directory: /path/to/boost_1_59_0 containing 'lib' (with the boost libraries) and 'boost' (with the headers), just set the environmental variable BOOST_HOME to the above path. If you use bash, you can do: export BOOST_HOME=/path/to/boost_1_59_0 (replacing /path/to/boost_1_59_0 appropriately). Then wipe your build directory and run ccmake from scratch. It should now find your pre-installed Boost libraries. Cheers, Chris On 09/04/16 02:31, Victor Eijkhout wrote:
I can not find in the documentation how to specify the Boost library.
1. I’ve unzipped the tar.bz2 file in the ThirdParty directory, but nektar still tries to download the tar.bz2 file.
2. I have a boost 1.59 installed, and the bin directory is in the LD_LIBRARY_PATH but the installation is not finding or using it.
Victor.
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
export BOOST_HOME=/path/to/boost_1_59_0
Thanks. That helped for the cmake but not the make: -- Searching for Boost: -- -- Found Boost thread library: /opt/apps/intel16/boost/1.59/lib/libboost_thread.so -- -- Found Boost iostreams library: /opt/apps/intel16/boost/1.59/lib/libboost_iostreams.so -- -- Found Boost date_time library: /opt/apps/intel16/boost/1.59/lib/libboost_date_time.so -- -- Found Boost filesystem library: /opt/apps/intel16/boost/1.59/lib/libboost_filesystem.so -- -- Found Boost system library: /opt/apps/intel16/boost/1.59/lib/libboost_system.so -- -- Found Boost program_options library: /opt/apps/intel16/boost/1.59/lib/libboost_program_options.so -- -- Found Boost regex library: /opt/apps/intel16/boost/1.59/lib/libboost_regex.so -- -- Found Boost timer library: /opt/apps/intel16/boost/1.59/lib/libboost_timer.so -- Build boost libs: thread, iostreams, date_time, filesystem, system, program_options, regex, timer -- Looking for include file mpi.h -- Looking for include file mpi.h - not found -- Looking for MPI_Send -- Looking for MPI_Send - not found -- Found MPI_C: /usr/lib64/libdl.so;/opt/cray/mpt/default/gni/mpich-intel/14.0/lib/libmpich_intel.so;/usr/lib64/librt.so;/opt/cray/ugni/default/lib64/libugni.so;/opt/cray/pmi/default/lib64/libpmi.so;/usr/lib64/libdl.so;/opt/cray/xpmem/default/lib64/libxpmem.so;/usr/lib64/libpthread.so;/opt/cray/udreg/default/lib64/libudreg.so -- Found MPI_CXX: /usr/lib64/libdl.so;/opt/cray/mpt/default/gni/mpich-intel/14.0/lib/libmpichcxx_intel.so;/opt/cray/mpt/default/gni/mpich-intel/14.0/lib/libmpich_intel.so;/usr/lib64/librt.so;/opt/cray/ugni/default/lib64/libugni.so;/opt/cray/pmi/default/lib64/libpmi.so;/usr/lib64/libdl.so;/opt/cray/xpmem/default/lib64/libxpmem.so;/usr/lib64/libpthread.so;/opt/cray/udreg/default/lib64/libudreg.so -- Found MPI: /usr/lib64/libdl.so -- Build GSMPI: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libgsmpi.a -- Build XXT: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libxxt.a -- Found MKL: /opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/include -- Configuring done -- Generating done -- Build files have been written to: /work/00434/eijkhout/lonestar/nektar/build-4.3.0 make[1]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[2]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' Scanning dependencies of target boost make[3]: Leaving directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' [ 0%] Creating directories for 'boost' [ 1%] Performing download step (download, verify and extract) for 'boost' -- downloading... src='https://www.nektar.info/thirdparty/boost_1_57_0.tar.bz2' dst='/work/00434/eijkhout/lonestar/nektar/nektar++-4.3.0/ThirdParty/boost_1_57_0.tar.bz2' timeout='none' CMake Error at stamp/download-boost.cmake:27 (message): error: downloading 'https://www.nektar.info/thirdparty/boost_1_57_0.tar.bz2' failed
(replacing /path/to/boost_1_59_0 appropriately).
Then wipe your build directory and run ccmake from scratch. It should now find your pre-installed Boost libraries.
Cheers, Chris
On 09/04/16 02:31, Victor Eijkhout wrote:
I can not find in the documentation how to specify the Boost library.
1. I’ve unzipped the tar.bz2 file in the ThirdParty directory, but nektar still tries to download the tar.bz2 file.
2. I have a boost 1.59 installed, and the bin directory is in the LD_LIBRARY_PATH but the installation is not finding or using it.
Victor.
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Victor, Its worth double checking that the THIRDPARTY_BUILD_BOOST option in cmake is actually set to OFF. I assume this is probably already set correctly since your existing Boost installation has now been picked up but if THIRDPARTY_BUILD_BOOST is set to ON, this would explain why it is still trying to build a separate version of Boost. Cheers, Jeremy On 9 Apr 2016, at 17:29, Victor Eijkhout <eijkhout@tacc.utexas.edu> wrote:
export BOOST_HOME=/path/to/boost_1_59_0
Thanks. That helped for the cmake but not the make:
-- Searching for Boost: -- -- Found Boost thread library: /opt/apps/intel16/boost/1.59/lib/libboost_thread.so -- -- Found Boost iostreams library: /opt/apps/intel16/boost/1.59/lib/libboost_iostreams.so -- -- Found Boost date_time library: /opt/apps/intel16/boost/1.59/lib/libboost_date_time.so -- -- Found Boost filesystem library: /opt/apps/intel16/boost/1.59/lib/libboost_filesystem.so -- -- Found Boost system library: /opt/apps/intel16/boost/1.59/lib/libboost_system.so -- -- Found Boost program_options library: /opt/apps/intel16/boost/1.59/lib/libboost_program_options.so -- -- Found Boost regex library: /opt/apps/intel16/boost/1.59/lib/libboost_regex.so -- -- Found Boost timer library: /opt/apps/intel16/boost/1.59/lib/libboost_timer.so -- Build boost libs: thread, iostreams, date_time, filesystem, system, program_options, regex, timer -- Looking for include file mpi.h -- Looking for include file mpi.h - not found -- Looking for MPI_Send -- Looking for MPI_Send - not found -- Found MPI_C: /usr/lib64/libdl.so;/opt/cray/mpt/default/gni/mpich-intel/14.0/lib/libmpich_intel.so;/usr/lib64/librt.so;/opt/cray/ugni/default/lib64/libugni.so;/opt/cray/pmi/default/lib64/libpmi.so;/usr/lib64/libdl.so;/opt/cray/xpmem/default/lib64/libxpmem.so;/usr/lib64/libpthread.so;/opt/cray/udreg/default/lib64/libudreg.so -- Found MPI_CXX: /usr/lib64/libdl.so;/opt/cray/mpt/default/gni/mpich-intel/14.0/lib/libmpichcxx_intel.so;/opt/cray/mpt/default/gni/mpich-intel/14.0/lib/libmpich_intel.so;/usr/lib64/librt.so;/opt/cray/ugni/default/lib64/libugni.so;/opt/cray/pmi/default/lib64/libpmi.so;/usr/lib64/libdl.so;/opt/cray/xpmem/default/lib64/libxpmem.so;/usr/lib64/libpthread.so;/opt/cray/udreg/default/lib64/libudreg.so -- Found MPI: /usr/lib64/libdl.so -- Build GSMPI: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libgsmpi.a -- Build XXT: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libxxt.a -- Found MKL: /opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/include -- Configuring done -- Generating done -- Build files have been written to: /work/00434/eijkhout/lonestar/nektar/build-4.3.0 make[1]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[2]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' Scanning dependencies of target boost make[3]: Leaving directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' [ 0%] Creating directories for 'boost' [ 1%] Performing download step (download, verify and extract) for 'boost' -- downloading... src='https://www.nektar.info/thirdparty/boost_1_57_0.tar.bz2' dst='/work/00434/eijkhout/lonestar/nektar/nektar++-4.3.0/ThirdParty/boost_1_57_0.tar.bz2' timeout='none' CMake Error at stamp/download-boost.cmake:27 (message): error: downloading 'https://www.nektar.info/thirdparty/boost_1_57_0.tar.bz2' failed
(replacing /path/to/boost_1_59_0 appropriately).
Then wipe your build directory and run ccmake from scratch. It should now find your pre-installed Boost libraries.
Cheers, Chris
On 09/04/16 02:31, Victor Eijkhout wrote:
I can not find in the documentation how to specify the Boost library.
1. I’ve unzipped the tar.bz2 file in the ThirdParty directory, but nektar still tries to download the tar.bz2 file.
2. I have a boost 1.59 installed, and the bin directory is in the LD_LIBRARY_PATH but the installation is not finding or using it.
Victor.
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
On Apr 9, 2016, at 4:51 AM, Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:
export BOOST_HOME=/path/to/boost_1_59_0
That stuff is not actually in the manual, right? Or am I looking at the wrong user guide? I could use some help with GSMPI. Since the package does not come with any build instructions I’m trying to use the stuff in the 3rd party directory. Cmake succeeds in building it: -- Build GSMPI: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libgsmpi.a -- Build XXT: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libxxt.a -- Found MKL: /opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/include -- Configuring done -- Generating done But then make tries to download it again: make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' Scanning dependencies of target gsmpi-1.2 make[3]: Leaving directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' [ 1%] Creating directories for 'gsmpi-1.2' [ 1%] Performing download step (download, verify and extract) for 'gsmpi-1.2' -- downloading... src='https://www.nektar.info/thirdparty/gsmpi-1.2.tar.bz2' dst='/work/00434/eijkhout/lonestar/nektar/nektar++-4.3.0/ThirdParty/gsmpi-1.2.tar.bz2' timeout='none' CMake Error at /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/stamp/download-gsmpi-1.2.cmake:27 (message): error: downloading 'https://www.nektar.info/thirdparty/gsmpi-1.2.tar.bz2' I can actually fix this by 1. letting Cmake build GSMPI and crash when failing to download it, and then 2. rerunning Cmake with BUILD_GSMPI:OFF. And then I crash on modmetis…. Victor.
Hi Victor, Can you download the gsmpi-1.2.tar.gz file manually in a web-browser or using "wget"? The error occurring is: "error: downloading 'https://www.nektar.info/thirdparty/gsmpi-1.2.tar.bz2'" which suggests there is a problem with your internet connection. Cheers, Chris On 11/04/16 21:11, Victor Eijkhout wrote:
On Apr 9, 2016, at 4:51 AM, Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:
export BOOST_HOME=/path/to/boost_1_59_0
That stuff is not actually in the manual, right? Or am I looking at the wrong user guide?
I could use some help with GSMPI.
Since the package does not come with any build instructions I’m trying to use the stuff in the 3rd party directory. Cmake succeeds in building it:
-- Build GSMPI: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libgsmpi.a -- Build XXT: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libxxt.a -- Found MKL: /opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/include -- Configuring done -- Generating done
But then make tries to download it again:
make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' Scanning dependencies of target gsmpi-1.2 make[3]: Leaving directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' make[3]: Entering directory `/work/00434/eijkhout/lonestar/nektar/build-4.3.0' [ 1%] Creating directories for 'gsmpi-1.2' [ 1%] Performing download step (download, verify and extract) for 'gsmpi-1.2' -- downloading... src='https://www.nektar.info/thirdparty/gsmpi-1.2.tar.bz2' dst='/work/00434/eijkhout/lonestar/nektar/nektar++-4.3.0/ThirdParty/gsmpi-1.2.tar.bz2' timeout='none' CMake Error at /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/stamp/download-gsmpi-1.2.cmake:27 (message): error: downloading 'https://www.nektar.info/thirdparty/gsmpi-1.2.tar.bz2'
I can actually fix this by 1. letting Cmake build GSMPI and crash when failing to download it, and then 2. rerunning Cmake with BUILD_GSMPI:OFF.
And then I crash on modmetis….
Victor.
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
On Apr 11, 2016, at 3:53 PM, Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:
Can you download the gsmpi-1.2.tar.gz file manually in a web-browser or using "wget”?
Yes I can. And then put it where? Specify how? Anyway: cmake has already found it:
-- Build GSMPI: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libgsmpi.a
So I don’t understand why make is subsequently downloading it again. Victor.
Hi Victor, On 12/04/16 05:57, Victor Eijkhout wrote:
On Apr 11, 2016, at 3:53 PM, Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:
Can you download the gsmpi-1.2.tar.gz file manually in a web-browser or using "wget”?
Yes I can. And then put it where? Specify how?
Anyway: cmake has already found it:
-- Build GSMPI: /work/00434/eijkhout/lonestar/nektar/build-4.3.0/ThirdParty/dist/lib/libgsmpi.a
So I don’t understand why make is subsequently downloading it again.
CMake is just saying it *will* build it from source by downloading it and compiling it when you type 'make'. It has not downloaded the file yet. The path is just the location where the library will be found once it is compiled. I am guessing you are building this on a cluster. The message is suggesting that there is a download error when it tries to get the file, such as it is unable to make an outgoing HTTPS connection to the web-server. This is why I am asking you to check if you can download the file *on the cluster* using wget to see if this is the problem. You could try downloading the files manually and putting them in the nektar++/ThirdParty directory. Assuming the file hashes match, it should not try to download them again. Cheers, Chris -- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
participants (3)
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Chris Cantwell
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Jeremy Cohen
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Victor Eijkhout