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Installation issue: gdal #12586
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Description
@adamjstewart if I understand the error correctly, it appears that if any of gdal's dependencies have MPI enabled, MPI must be loaded for libgdal to link correctly. Specifically, I propose we add an mpi variant to gdal and maybe couple it to enable/disable all the mpi aware dependencies of gdal. Does that make sense? If so I can create a pull request with the change.
Steps to reproduce the issue
$ spack env status
==> Using spack.yaml in current directory: /shared/stormcenter/Shen/src/MEX-2.3.0
$ spack install # see spack.yaml below
...
>> 3041 /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
al.so: undefined reference to `ompi_mpi_cxx_op_intercept'
>> 3042 /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
al.so: undefined reference to `MPI::Datatype::Free()'
>> 3043 /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
al.so: undefined reference to `MPI::Comm::Comm()'
>> 3044 /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
al.so: undefined reference to `MPI::Win::Free()'
>> 3045 collect2: error: ld returned 1 exit status
>> 3046 make[1]: *** [gdalinfo] Error 1
3047 make[1]: *** Waiting for unfinished jobs....
3048 make[1]: Leaving directory `/tmp/xis14008/spack-stage/spack-stage-
5eNDNt/spack-src/apps'
>> 3049 make: *** [apps-target] Error 2
See build log for details:
/shared/stormcenter/Shen/src/spack/var/spack/stage/gdal-3.0.1-4mvstpuneibqvhr45imvl3waobwa5hx6/spack-build-out.txtAttached the full log file [2.3 MB]: spack-build-out.txt
Platform and user environment
Please report your OS here:
$ uname -a
Linux cn01 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Nov 23 16:03:01 EST 2016 x86_64 x86_64 x86_64 GNU/Linux
$ lsb_release -d
Description: Red Hat Enterprise Linux Server release 6.7 (Santiago)
# ~/.spack/linux/compilers.yaml
compilers:
- compiler:
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: rhel6
paths:
cc: /usr/bin/gcc
cxx: /usr/bin/g++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: [email protected]
target: x86_64
- compiler:
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: rhel6
paths:
cc: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/gcc
cxx: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/g++
f77: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/gfortran
fc: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/gfortran
spec: [email protected]
target: x86_64# spack.yaml
# This is a Spack Environment file.
#
# It describes a set of packages to be installed, along with
# configuration settings.
spack:
# add package specs to the `specs` list
specs:
- gdal +hdf4 +hdf5 +jasper +netcdf +crypto +grib +curl ^hdf5 +hl ^openmpi +pmi fabrics=auto
%[email protected]
view: false
mirrors: {}
repos: []
upstreams: {}
modules:
enable: []
definitions: []
packages:
cmake:
buildable: false
paths:
[email protected]: /apps2/cmake/3.10.2
version: []
providers: {}
modules: {}
compiler: []
gmake:
buildable: false
paths:
[email protected]: /usr
version: []
providers: {}
modules: {}
compiler: []
config: {}Additional information
$ spack concretize -f
==> Concretized gdal+crypto+curl+grib+hdf4+hdf5+jasper+netcdf ^hdf5+hl ^openmpi%[email protected] fabrics=auto +pmi
- 4mvstpu [email protected]%[email protected]~armadillo~cfitsio+crypto~cryptopp+curl~expat~geos~gif+grib+hdf4+hdf5+jasper~java+jpeg~kea~libiconv+liblzma+libtool+libz~mdb+netcdf~odbc~opencl~openjpeg~pcre~perl~pg~png~poppler+proj~python~qhull~sosi~sqlite3~xerces~xml2~zstd arch=linux-rhel6-x86_64
[+] 4vx5fvr ^[email protected]%[email protected]~darwinssl~gssapi~libssh~libssh2~nghttp2 arch=linux-rhel6-x86_64
[+] b6r6fnb ^[email protected]%[email protected]+systemcerts arch=linux-rhel6-x86_64
[+] w4idrsb ^[email protected]%[email protected]+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-rhel6-x86_64
[+] qn2pvbe ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] gt74ike ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] rqwrhpn ^[email protected]%[email protected]~symlinks~termlib arch=linux-rhel6-x86_64
[+] cmluutb ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] rjqs3cq ^[email protected]%[email protected]+optimize+pic+shared arch=linux-rhel6-x86_64
[+] yyiyegm ^[email protected]%[email protected]~guile+nls patches=ca60bd9c1a1b35bc0dc58b6a4a19d5c2651f7a94a4b22b2c5ea001a1ca7a8a7f arch=linux-rhel6-x86_64
[+] lyr63eg ^[email protected]%[email protected]~szip arch=linux-rhel6-x86_64
[+] hseynw6 ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] iej2wmo ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] opcp74a ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] twor3y6 ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-rhel6-x86_64
[+] x33qfwi ^[email protected]%[email protected]+shared arch=linux-rhel6-x86_64
[+] mw4lps6 ^[email protected]%[email protected]~python arch=linux-rhel6-x86_64
[+] aso4k7z ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] o2xme3g ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] hhxm2xj ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] h3gzxvn ^[email protected]%[email protected] patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-rhel6-x86_64
[+] kuyi76p ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] jay4qjn ^[email protected]%[email protected]+lex patches=09c22e5c6fef327d3e48eb23f0d610dcd3a35ab9207f12e0f875701c677978d3 arch=linux-rhel6-x86_64
[+] 3crh7lk ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] 6j77nxv ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] of3s2pk ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] pu7o7ls ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] enxs2ae ^[email protected]%[email protected]~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-rhel6-x86_64
[+] 5f2wqfv ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] u2ffeby ^[email protected]%[email protected]~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-rhel6-x86_64
[+] oxprqis ^[email protected]%[email protected]~cuda+cxx_exceptions fabrics=auto ~java~legacylaunchers~memchecker+pmi schedulers=none ~sqlite3~thread_multiple+vt arch=linux-rhel6-x86_64
[+] njk5j57 ^[email protected]%[email protected]~cairo~cuda~gl+libxml2~nvml+pci+shared arch=linux-rhel6-x86_64
[+] bkmqzbd ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] 5u6bbgi ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] nxxlgnc ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] e2ecn35 ^[email protected]%[email protected] build_type=Release +jpeg~opengl patches=95a654159688eaffdf035a467914c5953068ad0fd62d18229de5779a17ec380b,db104400a2e72f610b8fa4d061a32282254819c70b024ef1cf99fef64aca67e3 +shared arch=linux-rhel6-x86_64
[+] qsmbnxo ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] l5srte6 ^[email protected]%[email protected]+jpeg patches=9485efc0a62a02207d34ac0c4d22e421c975b6ce85397c5e557c0105a232aaa3,ac81bd50db5950b42e48de78845ad91c60bc107ccaa1acd78836e03fdf4a2313,e0d45d3c34bf92df2d1d140957f110dc84759420e68a97e1e3d6ab90c81777d8 +proj+zlib arch=linux-rhel6-x86_64
[+] poxlp53 ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] 25tmaus ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+] qpmcb6k ^[email protected]%[email protected]+fts~functions arch=linux-rhel6-x86_64
[+] gxgix6l ^[email protected]%[email protected]~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf patches=10a1c3f7fa05e2c82457482e272bbe04d66d0047b237ad0a73e87d63d848b16c +pic+shared arch=linux-rhel6-x86_64Reactions are currently unavailable