Conda: librt.so needed
aosterthun opened this issue · comments
Hello,
I wanted to use conan at one point (#91), since I couldn't get it to work on my own, I used a global netcdf-cxx4 install for now. I recently started to use conda for python dependencies and found out that one can use conda for c++ as well. So I found that there is a netcdf-cxx4 package in conda-forge.
I tried using that, and it kinda works in regards to finding the headers and lib files, but I get another error when compiling my executable:
make[2]: *** No rule to make target '/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/librt.so', needed by 'netcdf_cxx'. Stop.
My cmake file looks like this:
cmake_minimum_required(VERSION 3.14)
project(raframe)
find_package(netCDF)
include_directories(~/miniconda3/envs/raframe/include)
add_executable(netcdf_cxx examples/netcdf_cxx.cpp)
target_link_libraries(netcdf_cxx netCDF::netcdf)And my conda environment contains the following packages:
# packages in environment at /home/arneo/miniconda3/envs/raframe:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
binutils_impl_linux-64 2.31.1 h6176602_1
binutils_linux-64 2.31.1 h6176602_9
bzip2 1.0.8 h516909a_2 conda-forge/label/cf202003
ca-certificates 2019.11.28 hecc5488_0 conda-forge/label/cf202003
curl 7.68.0 hf8cf82a_0 conda-forge/label/cf202003
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_9
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_9
hdf4 4.2.13 hf30be14_1003 conda-forge/label/cf202003
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge/label/cf202003
jpeg 9c h14c3975_1001 conda-forge/label/cf202003
krb5 1.16.4 h2fd8d38_0 conda-forge/label/cf202003
libcurl 7.68.0 hda55be3_0 conda-forge/label/cf202003
libedit 3.1.20170329 hf8c457e_1001 conda-forge/label/cf202003
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge/label/cf202003
libnetcdf 4.7.3 nompi_h9f9fd6a_101 conda-forge/label/cf202003
libssh2 1.8.2 h22169c7_2 conda-forge/label/cf202003
libstdcxx-ng 9.1.0 hdf63c60_0
ncurses 6.1 hf484d3e_1002 conda-forge/label/cf202003
netcdf-cxx4 4.3.1 nompi_h6006711_102 conda-forge/label/cf202003
openssl 1.1.1e h516909a_0 conda-forge/label/cf202003
tk 8.6.10 hed695b0_0 conda-forge/label/cf202003
zlib 1.2.11 h516909a_1006 conda-forge/label/cf202003
Any hints on why I get this error ? Since the conda package for netcdf-cxx4 has been downloaded over 30000 times I guess this is a system specific issue ?
Interesting. It looks like the librt library (system runtime library) is missing from the environment. I'm not sure if this is something that conda would install or if it is assumed it would be part of the system-wide development kit. I've done a little bit of searching, and I see it is related to libc. I'm not entirely certain why there is a dependency on librt for netcdf-cxx4.
A little more searching turned up that librt contains functions for Real Time Solaris. Are you working on Solaris, and if so are you able to install librt using the system (or conda) package manager?
I'm working on Manjaro with the XFCE desktop environment. I havn't been able to find librt in either conda nor pacman or the AUR.
Yeah it's really weird. Would it help if I tried to build netcdf from source to see if I can reproduce the error when building the library myself ? But since I'm able to install the lib through pamac install netcdf-cxx there shouldn't be a problem building the lib in general.
I found that there exists a similar error in conan: conan-io/conan#3972. Maybe this is the same underlying issue.
Interesting, thanks for the link, I'm reading through that now. If you're able to try building from source and willing to report back if you encounter the same error, I would very much appreciate it. Also, what is the output if you run ldd on the netcdf-cxx4 library installed by conda, out of curiosity?
I had to change OS I'm now on:
Distributor ID: Ubuntu
Description: Ubuntu 18.04.5 LTS
Release: 18.04
Codename: bionic
But I get the same error. For Ubuntu I don't need to test building manually because I already did that once and had no problem with that.
ldd output for libnetcdf_c++4.so:
linux-vdso.so.1 (0x00007ffca8fc7000)
libnetcdf.so.18 => /home/arne/miniconda3/lib/./libnetcdf.so.18 (0x00007fa5e32b6000)
libstdc++.so.6 => /home/arne/miniconda3/lib/./libstdc++.so.6 (0x00007fa5e30bf000)
libgcc_s.so.1 => /home/arne/miniconda3/lib/./libgcc_s.so.1 (0x00007fa5e32a2000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa5e2cce000)
libmfhdf.so.0 => /home/arne/miniconda3/lib/././libmfhdf.so.0 (0x00007fa5e325e000)
libdf.so.0 => /home/arne/miniconda3/lib/././libdf.so.0 (0x00007fa5e2c1f000)
libhdf5_hl.so.100 => /home/arne/miniconda3/lib/././libhdf5_hl.so.100 (0x00007fa5e2bfa000)
libhdf5.so.103 => /home/arne/miniconda3/lib/././libhdf5.so.103 (0x00007fa5e2876000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa5e2657000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa5e22b9000)
libcurl.so.4 => /home/arne/miniconda3/lib/././libcurl.so.4 (0x00007fa5e222a000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa5e3233000)
libjpeg.so.9 => /home/arne/miniconda3/lib/./././libjpeg.so.9 (0x00007fa5e21ec000)
libz.so.1 => /home/arne/miniconda3/lib/./././libz.so.1 (0x00007fa5e21cc000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fa5e1fc4000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa5e1dc0000)
libnghttp2.so.14 => /home/arne/miniconda3/lib/./././libnghttp2.so.14 (0x00007fa5e1d98000)
libssh2.so.1 => /home/arne/miniconda3/lib/./././libssh2.so.1 (0x00007fa5e1d52000)
libssl.so.1.1 => /home/arne/miniconda3/lib/./././libssl.so.1.1 (0x00007fa5e1cc2000)
libcrypto.so.1.1 => /home/arne/miniconda3/lib/./././libcrypto.so.1.1 (0x00007fa5e19f6000)
libgssapi_krb5.so.2 => /home/arne/miniconda3/lib/./././libgssapi_krb5.so.2 (0x00007fa5e19a7000)
libkrb5.so.3 => /home/arne/miniconda3/lib/./././libkrb5.so.3 (0x00007fa5e18ce000)
libk5crypto.so.3 => /home/arne/miniconda3/lib/./././libk5crypto.so.3 (0x00007fa5e18af000)
libcom_err.so.3 => /home/arne/miniconda3/lib/./././libcom_err.so.3 (0x00007fa5e18a9000)
libkrb5support.so.0 => /home/arne/miniconda3/lib/././././libkrb5support.so.0 (0x00007fa5e1898000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fa5e167d000)
And ldd output for libnetcdf.so:
linux-vdso.so.1 (0x00007ffe96290000)
libmfhdf.so.0 => /home/arne/miniconda3/lib/./libmfhdf.so.0 (0x00007f776e9a4000)
libdf.so.0 => /home/arne/miniconda3/lib/./libdf.so.0 (0x00007f776e84f000)
libhdf5_hl.so.100 => /home/arne/miniconda3/lib/./libhdf5_hl.so.100 (0x00007f776e97f000)
libhdf5.so.103 => /home/arne/miniconda3/lib/./libhdf5.so.103 (0x00007f776e4cb000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f776e2ac000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f776df0e000)
libcurl.so.4 => /home/arne/miniconda3/lib/./libcurl.so.4 (0x00007f776de7f000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f776da8e000)
libjpeg.so.9 => /home/arne/miniconda3/lib/././libjpeg.so.9 (0x00007f776e927000)
libz.so.1 => /home/arne/miniconda3/lib/././libz.so.1 (0x00007f776da6e000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f776d866000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f776d662000)
/lib64/ld-linux-x86-64.so.2 (0x00007f776e8fe000)
libnghttp2.so.14 => /home/arne/miniconda3/lib/././libnghttp2.so.14 (0x00007f776d63a000)
libssh2.so.1 => /home/arne/miniconda3/lib/././libssh2.so.1 (0x00007f776d5f6000)
libssl.so.1.1 => /home/arne/miniconda3/lib/././libssl.so.1.1 (0x00007f776d566000)
libcrypto.so.1.1 => /home/arne/miniconda3/lib/././libcrypto.so.1.1 (0x00007f776d29a000)
libgssapi_krb5.so.2 => /home/arne/miniconda3/lib/././libgssapi_krb5.so.2 (0x00007f776d24b000)
libkrb5.so.3 => /home/arne/miniconda3/lib/././libkrb5.so.3 (0x00007f776d172000)
libk5crypto.so.3 => /home/arne/miniconda3/lib/././libk5crypto.so.3 (0x00007f776d151000)
libcom_err.so.3 => /home/arne/miniconda3/lib/././libcom_err.so.3 (0x00007f776d14b000)
libkrb5support.so.0 => /home/arne/miniconda3/lib/./././libkrb5support.so.0 (0x00007f776d13c000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f776cf21000)
I'm not sure, but I had problems in conan with using a wrong gcc/g++ when linking a SQLite library. Maybe the netcdf library in conda is build with a different gcc/g++ version.
I'm using gcc (Ubuntu 8.4.0-1ubuntu1~18.04) 8.4.0 and g++ (Ubuntu 8.4.0-1ubuntu1~18.04) 8.4.0.