search

OpenMS / contrib

Automated CMake build scripts for the OpenMS contrib libraries
Other
0 stars 21 forks source link

Eigen Fails to Install #90

Closed singjc closed 5 years ago

singjc commented 5 years ago

Hi,

I am running into an error when building contrib dependencies, specifically for Eigen.

CMake Command

[singjust@gra-login1 test-build]$ cmake -DBUILD_TYPE=EIGEN ../contrib

-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/custom/bin/cc
-- Check for working C compiler: /cvmfs/soft.computecanada.ca/custom/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/c++
-- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- ADDRESSMODEL is: 64-bit
-- BUILD_TYPE: EIGEN (one of: ALL;SEQAN;LIBSVM;XERCESC;BOOST;COINOR;BZIP2;ZLIB;GLPK;EIGEN;WILDMAGIC;SQLITE;KISSFFT;HDF5)
-- FORCE_REBUILD: OFF
-- NUMBER_OF_JOBS: 2 (maximal number of concurrent compile jobs)
-- Downloading EIGEN .. Try #1
-- Downloading EIGEN .. done
-- Validating archive for EIGEN .. 
-- Validating archive for EIGEN .. successful
-- Extracting EIGEN .. 
-- Extracting EIGEN .. done
-- Try patching /home/singjust/projects/def-hroest/bin/openms/build/test/test-build/src/eigen-eigen-5a0156e40feb/CMakeLists.txt with binary option ... 
-- Patching /home/singjust/projects/def-hroest/bin/openms/build/test/test-build/src/eigen-eigen-5a0156e40feb/CMakeLists.txt ... done
-- Try patching /home/singjust/projects/def-hroest/bin/openms/build/test/test-build/src/eigen-eigen-5a0156e40feb/blas/CMakeLists.txt with binary option ... 
-- Patching /home/singjust/projects/def-hroest/bin/openms/build/test/test-build/src/eigen-eigen-5a0156e40feb/blas/CMakeLists.txt ... done
-- Try patching /home/singjust/projects/def-hroest/bin/openms/build/test/test-build/src/eigen-eigen-5a0156e40feb/unsupported/CMakeLists.txt with binary option ... 
-- Patching /home/singjust/projects/def-hroest/bin/openms/build/test/test-build/src/eigen-eigen-5a0156e40feb/unsupported/CMakeLists.txt ... done
-- Generating eigen build system .. 
-- Generating eigen build system .. done
-- Installing eigen headers .. 
CMake Error at libraries.cmake/eigen.cmake:77 (message):
  Installing eigen headers ..  failed
Call Stack (most recent call first):
  CMakeLists.txt:587 (OPENMS_CONTRIB_BUILD_EIGEN)

-- Configuring incomplete, errors occurred!
See also "/home/singjust/projects/def-hroest/bin/openms/build/test/test-build/CMakeFiles/CMakeOutput.log".

contrib_build.log

-- Starting to build contrib --
CXX: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/c++
CC: /cvmfs/soft.computecanada.ca/custom/bin/cc

 ------------------------------------------------------------------------
                              eigen
 ------------------------------------------------------------------------

-- Standard libraries to link to explicitly: none
-- Could NOT find CHOLMOD (missing:  CHOLMOD_INCLUDES CHOLMOD_LIBRARIES)
-- Could NOT find UMFPACK (missing:  UMFPACK_INCLUDES UMFPACK_LIBRARIES)
-- Could NOT find SUPERLU (missing:  SUPERLU_INCLUDES SUPERLU_LIBRARIES SUPERLU_VERSION_OK)
-- A version of Pastix has been found but pastix_nompi.h does not exist in the include directory. Because Eigen tests require a version without MPI, we disable the Pastix backend.
--
-- Configured Eigen 3.3.4
--
-- Some things you can do now:
-- --------------+--------------------------------------------------------------
-- Command       |   Description
-- --------------+--------------------------------------------------------------
-- make install  | Install Eigen. Headers will be installed to:
--               |     <CMAKE_INSTALL_PREFIX>/<INCLUDE_INSTALL_DIR>
--               |   Using the following values:
--               |     CMAKE_INSTALL_PREFIX: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24
--               |     INCLUDE_INSTALL_DIR:  include/eigen3
--               |   Change the install location of Eigen headers using:
--               |     cmake . -DCMAKE_INSTALL_PREFIX=yourprefix
--               |   Or:
--               |     cmake . -DINCLUDE_INSTALL_DIR=yourdir
-- make doc      | Generate the API documentation, requires Doxygen & LaTeX
-- make check    | Build and run the unit-tests. Read this page:
--               |   http://eigen.tuxfamily.org/index.php?title=Tests
-- make blas     | Build BLAS library (not the same thing as Eigen)
-- make uninstall| Removes files installed by make install
-- --------------+--------------------------------------------------------------
--
-- Configuring done
-- Generating done
-- Build files have been written to: /project/6011811/bin/contrib-OpenMS_v24/src/eigen-eigen-5a0156e40feb/build
abort: repository /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/src/eigen-eigen-5a0156e40feb not found!
abort: repository /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/src/eigen-eigen-5a0156e40feb not found!
CMake Warning (dev) in bench/spbench/CMakeLists.txt:
  A logical block opening on the line

    /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/src/eigen-eigen-5a0156e40feb/bench/spbench/CMakeLists.txt:51 (if)

  closes on the line

    /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/src/eigen-eigen-5a0156e40feb/bench/spbench/CMakeLists.txt:63 (endif)

  with mis-matching arguments.
This warning is for project developers.  Use -Wno-dev to suppress it.

Install the project...
-- Install configuration: "Release"
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/signature_of_eigen3_matrix_library
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/share/pkgconfig/eigen3.pc
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/share/eigen3/cmake/Eigen3Targets.cmake
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/share/eigen3/cmake/UseEigen3.cmake
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/share/eigen3/cmake/Eigen3Config.cmake
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/share/eigen3/cmake/Eigen3ConfigVersion.cmake
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Cholesky
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/CholmodSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Core
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Dense
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Eigen
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Eigenvalues
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Geometry
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Householder
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/IterativeLinearSolvers
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Jacobi
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/LU
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/MetisSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/OrderingMethods
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/PaStiXSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/PardisoSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/QR
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/QtAlignedMalloc
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SPQRSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SVD
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/Sparse
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SparseCholesky
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SparseCore
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SparseLU
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SparseQR
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/StdDeque
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/StdList
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/StdVector
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/SuperLUSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/UmfPackSupport
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/src
-- Up-to-date: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/src/Householder
-- Installing: /home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/src/Householder/BlockHouseholder.h
CMake Error at Eigen/cmake_install.cmake:70 (file):
  file INSTALL cannot copy file
  "/home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/src/eigen-eigen-5a0156e40feb/Eigen/src/Householder/BlockHouseholder.h"
  to
  "/home/singjust/projects/def-hroest/bin/contrib-OpenMS_v24/include/eigen3/Eigen/src/Householder/BlockHouseholder.h".
Call Stack (most recent call first):
  cmake_install.cmake:69 (include)

gmake: *** [install] Error 1

@hroest and I briefly looked into it, we don't think disk space is the issue because there is more than enough disk space. Is there a possible conflict with the file ../include/eigen3/Eigen/Householder and the folder ../include/eigen3/Eigen/src/Householder?

If there is any other information you would like, please let me know.

Best,

Justin

singjc commented 5 years ago

It actually seems to compile correctly when I build it locally on my machine. It may be a space issue for the specific folder on our cluster maybe, I'm not sure.

CMake Command (Local Machine)

contrib-build$ cmake -DBUILD_TYPE=EIGEN .
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- ADDRESSMODEL is: 64-bit
-- BUILD_TYPE: EIGEN (one of: ALL;SEQAN;LIBSVM;XERCESC;BOOST;COINOR;BZIP2;ZLIB;GLPK;EIGEN;WILDMAGIC;SQLITE;KISSFFT;HDF5)
-- FORCE_REBUILD: OFF
-- NUMBER_OF_JOBS: 2 (maximal number of concurrent compile jobs)
-- Downloading EIGEN .. Try #1
-- Downloading EIGEN .. done
-- Validating archive for EIGEN .. 
-- Validating archive for EIGEN .. successful
-- Extracting EIGEN .. 
-- Extracting EIGEN .. done
-- Try patching /home/justincsing/dev/contrib-build/src/eigen-eigen-5a0156e40feb/CMakeLists.txt with binary option ... 
-- Patching /home/justincsing/dev/contrib-build/src/eigen-eigen-5a0156e40feb/CMakeLists.txt ... done
-- Try patching /home/justincsing/dev/contrib-build/src/eigen-eigen-5a0156e40feb/blas/CMakeLists.txt with binary option ... 
-- Patching /home/justincsing/dev/contrib-build/src/eigen-eigen-5a0156e40feb/blas/CMakeLists.txt ... done
-- Try patching /home/justincsing/dev/contrib-build/src/eigen-eigen-5a0156e40feb/unsupported/CMakeLists.txt with binary option ... 
-- Patching /home/justincsing/dev/contrib-build/src/eigen-eigen-5a0156e40feb/unsupported/CMakeLists.txt ... done
-- Generating eigen build system .. 
-- Generating eigen build system .. done
-- Installing eigen headers .. 
-- Installing eigen headers .. done
-- 
-- 
--   EIGEN has been built! Some parts of the contrib might still need (re)building.
--   Configure and build OpenMS at your discretion!
-- 
-- 
-- 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/justincsing/dev/contrib-build
hroest commented 5 years ago

@singjc I just tried this on graham cluster and it works on scratch -- can you try this on scratch as well and report back?

singjc commented 5 years ago

@hroest I am able to successfully build on scratch as well. It most likely is a space issue as you mentioned, we probably reached the max number of files/bytes for ./bin/.

hroest commented 5 years ago

@singjc I just tried this on graham cluster and it works on scratch -- can you try this on scratch as well and report back?