py-numpy linking to intel mkl while compiling with gcc and openblas? #5327
Description
I was bit confused by libmkl_rt in gcc compiled numpy:
$ find /gpfs/bbp.cscs.ch/scratch/gss/bgq/kumbhar-adm/SPACK_HOME/install_home/bbpviz_full/install/linux-rhel6-x86_64/gcc-5.3.0/py-numpy-1.13.1-lhfffv6h/ -name "*.so" -exec ldd {} \; -exec grep mkl {} \;
linux-vdso.so.1 => (0x00007fff38112000)
.......
Binary file /gpfs/bbp.cscs.ch/scratch/gss/bgq/kumbhar-adm/SPACK_HOME/install_home/bbpviz_full/install/linux-rhel6-x86_64/gcc-5.3.0/py-numpy-1.13.1-lhfffv6h/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so matches
linux-vdso.so.1 => (0x00007ffc5bfba000)
libmkl_rt.so => not found
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff4906df000)
Looking into spec we don't see any Intel or MKL dependency :
$ spack spec -y /lhfffv6h
spec:
- py-numpy:
version: 1.13.1
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
blas: true
lapack: true
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
dependencies:
openblas:
hash: tgtgdmq2dgjfvktxmizfo3gadxkerjxc
type:
- build
- link
python:
hash: dhkjobmenmlls3dqb2xf3vel22fdrczc
type:
- build
- link
- run
hash: lhfffv6hlf5d5hnljecb574ocevmvbhq
- openblas:
version: 0.2.20
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
openmp: true
pic: true
shared: true
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
hash: tgtgdmq2dgjfvktxmizfo3gadxkerjxc
- python:
version: 2.7.13
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
shared: true
tk: false
ucs4: false
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
dependencies:
bzip2:
hash: npjovariojv5p4pml2t6e3prwuvfpucy
type:
- build
- link
ncurses:
hash: drvhqydmzj53gsnf32gykluasamrtbbi
type:
- build
- link
openssl:
hash: hkpcjq2zk7qdrrjz35m44tzrpiikdu33
type:
- build
- link
readline:
hash: u2nuuoap42ogsgp3py4q7bjunqjyhlfl
type:
- build
- link
sqlite:
hash: g2xodjde4jxzbdijstqv3gqwv3tiwnfk
type:
- build
- link
zlib:
hash: cabzx2gna7p6g6tsll42c4q3aia2gx4e
type:
- build
- link
hash: dhkjobmenmlls3dqb2xf3vel22fdrczc
- bzip2:
version: 1.0.6
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
shared: true
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
hash: npjovariojv5p4pml2t6e3prwuvfpucy
- ncurses:
version: 5.7.4
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
symlinks: false
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
external:
module: false
path: /usr
hash: drvhqydmzj53gsnf32gykluasamrtbbi
- openssl:
version: '1.0'
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
external:
module: false
path: /usr
hash: hkpcjq2zk7qdrrjz35m44tzrpiikdu33
- readline:
version: 6.0.4
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
external:
module: false
path: /usr
hash: u2nuuoap42ogsgp3py4q7bjunqjyhlfl
- sqlite:
version: 3.6.20
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
external:
module: false
path: /usr
hash: g2xodjde4jxzbdijstqv3gqwv3tiwnfk
- zlib:
version: 1.2.11
arch:
platform: linux
platform_os: rhel6
target: x86_64
compiler:
name: gcc
version: 5.3.0
namespace: builtin
parameters:
pic: true
shared: true
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
hash: cabzx2gna7p6g6tsll42c4q3aia2gx4e
If I look at build.out then we see some MKL related stuff:
==> Executing phase: 'build'
==> '/gpfs/bbp.cscs.ch/scratch/gss/bgq/kumbhar-adm/SPACK_HOME/install_home/bbpviz_full/install/linux-rhel6-x86_64/gcc-5.3.0/python-2.7.13-dhkjobme/bin/python2.7' 'setup.py' '--no-user-cfg' 'build' '-j' '16'
Running from numpy source directory.
blas_opt_info:
blas_mkl_info:
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
include_dirs = ['/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl', '/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl/include', '/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl/lib']
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
include_dirs = ['/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl', '/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl/include', '/gpfs/bbp.cscs.ch/home/kumbhar-adm/SPACK_HOME/install_home/externals/install/linux-rhel6-x86_64/gcc-4.4.7/intel-parallel-studio-professional.2017.4/compilers_and_libraries_2017.4.196/linux/mkl/lib']
....
And if I look at build.env we have :
MIC_LD_LIBRARY_PATH=/some/mkl/path/
MIC_LIBRARY_PATH=/some/mkl/path/
MKLROOT=/some/mkl/path/
I assume we don't remove these variables like LD_LIBRARY_PATH and causing MKL getting linked to py-numpy? Or, anything obvious I am missing here?
EDIT: I confirm MKLROOT was set in my bash env.