libatomic.so.1 not found

[BinhongLiu]

Expected Behavior

Compile the specific version MMseqs2 71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1 (May 28, 2023) under Linux

I encounter a similar error as here. And the mentioned package libgcc-ng has been installed.

Current Behavior

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.

cd MMseqs2-71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1 mkdir build cd build cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. .. make make install export PATH=/home/liuhongbin/database/colabfoldMSA/MMseqs2-71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1/build/bin/:$PATH

no errors were observed here.

MMseqs Output (for bugs)

error:

(colabfoldMSA) liuhongbin@node7:~/database/colabfoldMSA/MMseqs2-71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1/build$ ./bin/mmseqs ./bin/mmseqs: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): 71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1

• Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):

• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: g++ (GCC) 5.4.0 cmake version 3.28.1

• Server specifications (especially CPU support for AVX2/SSE and amount of system memory): uname -a | grep x86_64 Linux node7 3.10.0-1160.11.1.el7.x86_64 #1 SMP Fri Dec 18 16:34:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

• Operating system and version: CentOS Linux release 8 (Core)

• packages in current environment `conda list packages in environment at /home/liuhongbin/anaconda3/envs/colabfoldMSA:

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge absl-py 1.4.0 pypi_0 pypi alphafold-colabfold 2.3.6 pypi_0 pypi appdirs 1.4.4 pypi_0 pypi astunparse 1.6.3 pypi_0 pypi binutils 2.40 hdd6e379_0 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge binutils_linux-64 2.40 hbdbef99_2 conda-forge biopython 1.82 pypi_0 pypi bzip2 1.0.8 hd590300_5 conda-forge c-compiler 1.7.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge cachetools 5.3.2 pypi_0 pypi certifi 2023.11.17 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi chex 0.1.85 pypi_0 pypi colabfold 1.5.5 pypi_0 pypi contextlib2 21.6.0 pypi_0 pypi contourpy 1.2.0 pypi_0 pypi cxx-compiler 1.7.0 h00ab1b0_0 conda-forge cycler 0.12.1 pypi_0 pypi dm-haiku 0.0.10 pypi_0 pypi dm-tree 0.1.8 pypi_0 pypi flatbuffers 23.5.26 pypi_0 pypi fonttools 4.47.0 pypi_0 pypi gast 0.5.4 pypi_0 pypi gcc 12.3.0 h8d2909c_2 conda-forge gcc_impl_linux-64 12.3.0 he2b93b0_3 conda-forge gcc_linux-64 12.3.0 h76fc315_2 conda-forge google-auth 2.26.1 pypi_0 pypi google-auth-oauthlib 1.2.0 pypi_0 pypi google-pasta 0.2.0 pypi_0 pypi grpcio 1.60.0 pypi_0 pypi gxx 12.3.0 h8d2909c_2 conda-forge gxx_impl_linux-64 12.3.0 he2b93b0_3 conda-forge gxx_linux-64 12.3.0 h8a814eb_2 conda-forge h5py 3.10.0 pypi_0 pypi idna 3.6 pypi_0 pypi immutabledict 4.1.0 pypi_0 pypi importlib-metadata 4.13.0 pypi_0 pypi jax 0.4.23 pypi_0 pypi jaxlib 0.4.23 pypi_0 pypi jmp 0.0.4 pypi_0 pypi keras 2.15.0 pypi_0 pypi kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge kiwisolver 1.4.5 pypi_0 pypi ld_impl_linux-64 2.40 h41732ed_0 conda-forge libclang 16.0.6 pypi_0 pypi libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libsanitizer 12.3.0 h0f45ef3_3 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libstdcxx-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge markdown 3.5.1 pypi_0 pypi markupsafe 2.1.3 pypi_0 pypi matplotlib 3.8.2 pypi_0 pypi ml-collections 0.1.1 pypi_0 pypi ml-dtypes 0.2.0 pypi_0 pypi ncurses 6.4 h59595ed_2 conda-forge numpy 1.26.3 pypi_0 pypi oauthlib 3.2.2 pypi_0 pypi openssl 3.2.0 hd590300_1 conda-forge opt-einsum 3.3.0 pypi_0 pypi packaging 23.2 pypi_0 pypi pandas 1.5.3 pypi_0 pypi pillow 10.2.0 pypi_0 pypi pip 23.3.2 pyhd8ed1ab_0 conda-forge protobuf 4.23.4 pypi_0 pypi py3dmol 2.0.4 pypi_0 pypi pyasn1 0.5.1 pypi_0 pypi pyasn1-modules 0.3.0 pypi_0 pypi pyparsing 3.1.1 pypi_0 pypi python 3.10.13 hd12c33a_1_cpython conda-forge python-dateutil 2.8.2 pypi_0 pypi pytz 2023.3.post1 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi readline 8.2 h8228510_1 conda-forge requests 2.31.0 pypi_0 pypi requests-oauthlib 1.3.1 pypi_0 pypi rsa 4.9 pypi_0 pypi scipy 1.11.4 pypi_0 pypi setuptools 69.0.3 pyhd8ed1ab_0 conda-forge six 1.16.0 pypi_0 pypi sysroot_linux-64 2.12 he073ed8_16 conda-forge tabulate 0.9.0 pypi_0 pypi tensorboard 2.15.1 pypi_0 pypi tensorboard-data-server 0.7.2 pypi_0 pypi tensorflow-cpu 2.15.0.post1 pypi_0 pypi tensorflow-estimator 2.15.0 pypi_0 pypi tensorflow-io-gcs-filesystem 0.35.0 pypi_0 pypi termcolor 2.4.0 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge toolz 0.12.0 pypi_0 pypi tqdm 4.66.1 pypi_0 pypi typing-extensions 4.9.0 pypi_0 pypi tzdata 2023d h0c530f3_0 conda-forge urllib3 2.1.0 pypi_0 pypi werkzeug 3.0.1 pypi_0 pypi wheel 0.42.0 pyhd8ed1ab_0 conda-forge wrapt 1.14.1 pypi_0 pypi xz 5.2.6 h166bdaf_0 conda-forge zipp 3.17.0 pypi_0 pypi`

[milot-mirdita]

If you use conda, please make sure to also use the conda-compilers and not your system compiler.

before calling cmake please do:

export CC=path-to-conda-gcc
export CXX=path-to-conda-g++