mpifort 5.0.1 fails with undefined refs to memcpy@GLIBC_2.14 and clock_gettime@GLIBC_2.17 #143
Description
Solution to issue cannot be found in the documentation.
- I checked the documentation.
Issue
I am using cmake, gfortran, and openmpi from conda-forge to compile a Fortran package. With cmake 3.28.3, gfortran 13.2.0 and openmpi 5.0.0 everything works. When openmpi upgraded to the latest 5.0.1 version I started getting this error:
-- Check for working Fortran compiler: /home/cgw/miniforge3/envs/mfix-git/bin/mpifort
-- Check for working Fortran compiler: /home/cgw/miniforge3/envs/mfix-git/bin/mpifort - broken
CMake Error at /home/cgw/miniforge3/envs/mfix-git/share/cmake-3.28/Modules/CMakeTestFortranCompiler.cmake:59 (message):
The Fortran compiler
"/home/cgw/miniforge3/envs/mfix-git/bin/mpifort"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: '/tmp/TTT/build_dmp/CMakeFiles/CMakeScratch/TryCompile-38w6ll'
Run Build Command(s): /home/cgw/miniforge3/envs/mfix-git/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile cmTC_6144f/fast
/usr/bin/gmake -f CMakeFiles/cmTC_6144f.dir/build.make CMakeFiles/cmTC_6144f.dir/build
gmake[1]: Entering directory '/tmp/TTT/build_dmp/CMakeFiles/CMakeScratch/TryCompile-38w6ll'
Building Fortran object CMakeFiles/cmTC_6144f.dir/testFortranCompiler.f.o
/home/cgw/miniforge3/envs/mfix-git/bin/mpifort -c /tmp/TTT/build_dmp/CMakeFiles/CMakeScratch/TryCompile-38w6ll/testFortranCompiler.f -o CMakeFiles/cmTC_6144f.dir/testFortranCompiler.f.o
Linking Fortran executable cmTC_6144f
/home/cgw/miniforge3/envs/mfix-git/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6144f.dir/link.txt --verbose=1
/home/cgw/miniforge3/envs/mfix-git/bin/mpifort CMakeFiles/cmTC_6144f.dir/testFortranCompiler.f.o -o cmTC_6144f
/home/cgw/miniforge3/envs/mfix-git/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/cgw/miniforge3/envs/mfix-git/lib/libmpi_mpifh.so: undefined reference to `memcpy@GLIBC_2.14'
/home/cgw/miniforge3/envs/mfix-git/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/cgw/miniforge3/envs/mfix-git/lib/./libpmix.so.2: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_6144f.dir/build.make:99: cmTC_6144f] Error 1
gmake[1]: Leaving directory '/tmp/TTT/build_dmp/CMakeFiles/CMakeScratch/TryCompile-38w6ll'
gmake: *** [Makefile:127: cmTC_6144f/fast] Error 2
Installed packages
# packages in environment at /home/cgw/miniforge3/envs/mfix-git:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiohttp 3.9.1 py310h2372a71_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.10 hd590300_0 conda-forge
aom 3.8.1 h59595ed_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
blinker 1.7.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.26.0 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cmake 3.28.3 hcfe8598_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py310hd41b1e2_0 conda-forge
curl 8.5.0 hca28451_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
docutils 0.20.1 py310hff52083_3 conda-forge
double-conversion 3.3.0 h59595ed_0 conda-forge
eigen 3.4.0 h00ab1b0_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
ffmpeg 6.1.1 gpl_h8007c5b_104 conda-forge
ffmpeg-python 0.2.0 py_0 conda-forge
flask 3.0.2 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.47.2 py310h2372a71_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
frozenlist 1.4.1 py310h2372a71_0 conda-forge
future 0.18.3 pyhd8ed1ab_0 conda-forge
gcc 13.2.0 h574f8da_2 conda-forge
gcc_impl_linux-64 13.2.0 h338b0a0_5 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gfortran 13.2.0 h0584b13_2 conda-forge
gfortran_impl_linux-64 13.2.0 h76e1118_5 conda-forge
git 2.43.0 pl5321h7bc287a_0 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.41 pyhd8ed1ab_0 conda-forge
gl2ps 1.4.2 h0708190_0 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glib 2.78.3 hfc55251_0 conda-forge
glib-tools 2.78.3 hfc55251_0 conda-forge
gmp 6.3.0 h59595ed_0 conda-forge
gnutls 3.7.9 hb077bed_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gst-plugins-base 1.22.9 h8e1006c_0 conda-forge
gstreamer 1.22.9 h98fc4e7_0 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_h4f84152_100 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.0.1 pyha770c72_0 conda-forge
itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
jsoncpp 1.9.5 h4bd325d_1 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230802.1 cxx17_h59595ed_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libass 0.17.1 h8fe9dca_1 conda-forge
libblas 3.9.0 21_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 21_linux64_openblas conda-forge
libclang 15.0.7 default_hb11cfb5_4 conda-forge
libclang13 15.0.7 default_ha2b6cf4_4 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.5.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libdrm 2.4.114 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libglib 2.78.3 h783c2da_0 conda-forge
libglu 9.0.0 hac7e632_1003 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libhwloc 2.9.3 default_h554bfaf_1009 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libidn2 2.3.7 hd590300_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 21_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libnetcdf 4.9.2 nompi_h9612171_113 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnl 3.9.0 hd590300_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge
libopenvino 2023.3.0 h2e90f83_0 conda-forge
libopenvino-auto-batch-plugin 2023.3.0 hd5fc58b_0 conda-forge
libopenvino-auto-plugin 2023.3.0 hd5fc58b_0 conda-forge
libopenvino-hetero-plugin 2023.3.0 h3ecfda7_0 conda-forge
libopenvino-intel-cpu-plugin 2023.3.0 h2e90f83_0 conda-forge
libopenvino-intel-gpu-plugin 2023.3.0 h2e90f83_0 conda-forge
libopenvino-ir-frontend 2023.3.0 h3ecfda7_0 conda-forge
libopenvino-onnx-frontend 2023.3.0 hfbc7f12_0 conda-forge
libopenvino-paddle-frontend 2023.3.0 hfbc7f12_0 conda-forge
libopenvino-pytorch-frontend 2023.3.0 h59595ed_0 conda-forge
libopenvino-tensorflow-frontend 2023.3.0 h0bff32c_0 conda-forge
libopenvino-tensorflow-lite-frontend 2023.3.0 h59595ed_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.17 h166bdaf_0 conda-forge
libpng 1.6.42 h2797004_0 conda-forge
libpq 16.1 h33b98f1_7 conda-forge
libprotobuf 4.25.1 hf27288f_1 conda-forge
libsanitizer 13.2.0 h7e041cc_5 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libsystemd0 255 h3516f8a_0 conda-forge
libtasn1 4.19.0 h166bdaf_0 conda-forge
libtheora 1.1.1 h7f98852_1005 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.46.0 hd590300_0 conda-forge
libva 2.20.0 hd590300_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libvpx 1.13.1 h59595ed_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.6.0 hd429924_1 conda-forge
libxml2 2.12.5 h232c23b_0 conda-forge
libzip 1.10.1 h2629f0a_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
loguru 0.7.2 py310hff52083_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
make 4.3 hd18ef5c_1 conda-forge
markupsafe 2.1.5 py310h2372a71_0 conda-forge
matplotlib 3.8.2 py310hff52083_0 conda-forge
matplotlib-base 3.8.2 py310h62c0568_0 conda-forge
mfix 23.3.2 0 https://private/conda/dist
mfix-doc 23.3.2 0 https://private/conda/dist
mfix-gui 23.3.2 py_0 https://private/conda/dist
mfix-solver 23.3.2 h3218e01_0 https://private/conda/dist
mfix-src 23.3.2 0 https://private/conda/dist
mpg123 1.32.4 h59595ed_0 conda-forge
mpi 1.0 openmpi conda-forge
mscorefonts 0.0.1 3 conda-forge
multidict 6.0.5 py310h2372a71_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nettle 3.9.1 h7ab15ed_0 conda-forge
nlohmann_json 3.11.2 h27087fc_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.97 h1d7d5a4_0 conda-forge
numpy 1.26.4 py310hb13e2d6_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openh264 2.4.1 h59595ed_0 conda-forge
openjpeg 2.5.0 h488ebb8_3 conda-forge
openmpi 5.0.1 h4970cb7_101 conda-forge
openssl 3.2.1 hd590300_0 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 10.2.0 py310h01dd4db_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
ply 3.11 py_1 conda-forge
proj 9.3.1 h1d62c97_0 conda-forge
psutil 5.9.8 py310h2372a71_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pugixml 1.14 h59595ed_0 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py310h04931ad_5 conda-forge
pyqt5-sip 12.12.2 py310hc6cd4ac_5 conda-forge
pyqtgraph 0.13.3 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.13 hd12c33a_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py310h2372a71_1 conda-forge
qt-main 5.15.8 h450f30e_18 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rhash 1.4.4 hd590300_0 conda-forge
setproctitle 1.3.3 py310h2372a71_0 conda-forge
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
simplejson 3.19.2 py310h2372a71_0 conda-forge
sip 6.7.12 py310hc6cd4ac_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sphinx 7.2.6 pyhd8ed1ab_0 conda-forge
sphinx-prompt 1.4.0 pyhd8ed1ab_0 conda-forge
sphinx-substitution-extensions 2022.2.16 pypi_0 pypi
sphinx_rtd_theme 2.0.0 pyha770c72_0 conda-forge
sphinxcontrib-applehelp 1.0.8 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.6 pyhd8ed1ab_0 conda-forge
sphinxcontrib-htmlhelp 2.0.5 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jquery 4.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-qthelp 1.0.7 pyhd8ed1ab_0 conda-forge
sphinxcontrib-serializinghtml 1.1.10 pyhd8ed1ab_0 conda-forge
sqlite 3.44.2 h2c6b66d_0 conda-forge
svt-av1 1.8.0 h59595ed_0 conda-forge
sysroot_linux-64 2.12 he073ed8_16 conda-forge
tbb 2021.11.0 h00ab1b0_1 conda-forge
tbb-devel 2021.11.0 h5ccd973_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py310h2372a71_1 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
unicodedata2 15.1.0 py310h2372a71_0 conda-forge
urllib3 2.2.0 pyhd8ed1ab_0 conda-forge
utfcpp 4.0.5 ha770c72_0 conda-forge
vtk 9.2.6 qt_py310h1234567_220 conda-forge
vtk-base 9.2.6 qt_py310h1234567_220 conda-forge
vtk-io-ffmpeg 9.2.6 qt_py310h1234567_220 conda-forge
werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wslink 1.12.4 pyhd8ed1ab_0 conda-forge
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 py310h2372a71_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forgeEnvironment info
active environment : mfix-git
active env location : /home/cgw/miniforge3/envs/mfix-git
shell level : 1
user config file : /home/cgw/.condarc
populated config files : /home/cgw/miniforge3/.condarc
/home/cgw/.condarc
conda version : 23.3.1
conda-build version : not installed
python version : 3.10.12.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.38=0
__linux=6.6.8=0
__unix=0=0
base environment : /home/cgw/miniforge3 (writable)
conda av data dir : /home/cgw/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/cgw/miniforge3/pkgs
/home/cgw/.conda/pkgs
envs directories : /home/cgw/miniforge3/envs
/home/cgw/.conda/envs
platform : linux-64
user-agent : conda/23.3.1 requests/2.31.0 CPython/3.10.12 Linux/6.6.8-gentoo gentoo/2.14 glibc/2.38
UID:GID : 103:1000
netrc file : None
offline mode : False