/.post.script: 75: /.post.script: cannot open /app/alphafold/docker/openmm.patch: No such file

[SomePersonSomeWhereInTheWorld]

On RHEL 8 with Anaconda Python 2022.03:

+ pip3 install -r /app/alphafold/requirements.txt --no-cache-dir
ERROR: Could not open requirements file: [Errno 2] No such file or directory: '/app/alphafold/requirements.txt'
+ cd /opt/conda/lib/python3.7/site-packages
/.post.script: 75: /.post.script: cannot open /app/alphafold/docker/openmm.patch: No such file
+ patch -p0
FATAL:   While performing build: while running engine: exit status 2
[user@server alphafold-v2.2.4]# ls -l /opt/conda
ls: cannot access '/opt/conda': No such file or directory

[prehensilecode]

The container is built using Ubuntu 18.04 as the base distro via Nvidia’s nvidia/cuda:11.1.1-cudnn8-runtime-ubuntu18.04 container image.

And the Python within the container uses Miniconda3-py37_4.12.0-Linux-x86_64, not Anaconda Python 2022.03.

The first error is:

ERROR: Could not open requirements file: [Errno 2] No such file or directory: '/app/alphafold/requirements.txt'

which seems to indicate that you are trying to run the commands in the .def file at the commandline of your host system. This will not work.

How exactly are you trying to build the container?

[SomePersonSomeWhereInTheWorld]

How exactly are you trying to build the container?

Just as the tutorial says: singularity build alphafold.sif singularity/Singularity.def

[prehensilecode]

What version of singularity/apptainer are you using?

[prehensilecode]

How exactly are you trying to build the container?

Just as the tutorial says: singularity build alphafold.sif singularity/Singularity.def

You need to sudo to run this build (as stated in the README).

[SomePersonSomeWhereInTheWorld]

What version of singularity/apptainer are you using?

3.7.1

How exactly are you trying to build the container?

Just as the tutorial says: singularity build alphafold.sif singularity/Singularity.def

You need to sudo to run this build (as stated in the README).

yes doing it as root

[SomePersonSomeWhereInTheWorld]

I also tried with non-root user, using sudo -U, exported TMP as well to a bigger space, same error maybe there's a clue somewhere in this

[me@node alphafold-v2.2.4]$ export TMPDIR=/local
[me@node alphafold-v2.2.4]$ sudo -E /burg/opt/singularity-3.7/bin/singularity build alphafold.sif singularity/Singularity.def
INFO:    Starting build...
Getting image source signatures
Copying blob a404e5416296 skipped: already exists  
Copying blob 391d07dd0009 skipped: already exists  
Copying blob cb7a4dc5cae3 skipped: already exists  
Copying blob 3f77a3e2807d skipped: already exists  
Copying blob 0f0ed9680ff1 skipped: already exists  
Copying blob e2250e4b9e64 skipped: already exists  
Copying blob 9cf40c59065f [--------------------------------------] 0.0b / 0.0b
Copying blob 5e609a938304 [--------------------------------------] 0.0b / 0.0b
Copying config 45a65f4d98 done  
Writing manifest to image destination
Storing signatures
2023/02/08 12:24:28  info unpack layer: sha256:a404e54162968593b8d92b571f3cdd673e4c9eab5d9be28d7c494595c0aa6682
2023/02/08 12:24:29  info unpack layer: sha256:391d07dd0009f93d13fb7b13dab2078ad0686953b6b398f66688c7204466df48
2023/02/08 12:24:29  info unpack layer: sha256:cb7a4dc5cae35387c4323a9d9855171616e61cd95711ce2b411ce03a03f349e6
2023/02/08 12:24:30  info unpack layer: sha256:3f77a3e2807d8cb8690b749c26d19e6e462743141b750330d311916f3c4857e9
2023/02/08 12:24:30  info unpack layer: sha256:0f0ed9680ff1f69ce856414b2c9cd4482d37b24147c07821faba7ae51d862a6d
2023/02/08 12:24:30  info unpack layer: sha256:e2250e4b9e6414e7df5d1f97abaa9fdfb5b5a97cef526f9bdf91b6623b076b6a
2023/02/08 12:25:05  info unpack layer: sha256:9cf40c59065f805dd01d0a204a6817daa6acf7034abaf92e9d950c73d7b4cb11
2023/02/08 12:25:05  info unpack layer: sha256:5e609a938304d690f0fcd860b736e8f6dd17933c4803e2e0af972fc61f2572fa
INFO:    Copying . to /local/build-temp-340487126/rootfs/app/alphafold
INFO:    Running post scriptlet
+ apt-get update
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Reading package lists... Done
+ DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential cmake cuda-command-line-tools-11-1 git hmmer kalign tzdata wget
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cmake-data cpp cpp-7 cuda-cudart-dev-11-1 cuda-cuobjdump-11-1 cuda-cupti-11-1
  cuda-cupti-dev-11-1 cuda-driver-dev-11-1 cuda-gdb-11-1 cuda-memcheck-11-1 cuda-nvcc-11-1 cuda-nvdisasm-11-1 cuda-nvprof-11-1
  cuda-sanitizer-11-1 dpkg-dev g++ g++-7 gcc gcc-7 gcc-7-base git-man libarchive13 libasan4 libatomic1 libbinutils libc-dev-bin libc6-dev
  libcc1-0 libcilkrts5 libcurl3-gnutls libcurl4 libdivsufsort3 libdpkg-perl liberror-perl libexpat1 libgcc-7-dev libgdbm-compat4 libgdbm5
  libgomp1 libgssapi-krb5-2 libicu60 libisl19 libitm1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 liblzo2-2 libmpc3
  libmpfr6 libmpx2 libnghttp2-14 libperl5.26 libpsl5 libquadmath0 librhash0 librtmp1 libstdc++-7-dev libtsan0 libubsan0 libuv1 libxml2
  linux-libc-dev make multiarch-support patch perl perl-modules-5.26 xz-utils
Suggested packages:
  binutils-doc cmake-doc ninja-build cpp-doc gcc-7-locales debian-keyring g++-multilib g++-7-multilib gcc-7-doc libstdc++6-7-dbg gcc-multilib
  manpages-dev autoconf automake libtool flex bison gdb gcc-doc gcc-7-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan4-dbg
  liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg gettext-base git-daemon-run | git-daemon-sysvinit git-doc
  git-el git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn hmmer-doc lrzip glibc-doc bzr gdbm-l10n krb5-doc krb5-user libstdc++-7-doc
  make-doc ed diffutils-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl
Recommended packages:
  fakeroot libalgorithm-merge-perl less ssh-client manpages manpages-dev libfile-fcntllock-perl liblocale-gettext-perl krb5-locales publicsuffix
  netbase
The following NEW packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu build-essential cmake cmake-data cpp cpp-7 cuda-command-line-tools-11-1
  cuda-cudart-dev-11-1 cuda-cuobjdump-11-1 cuda-cupti-11-1 cuda-cupti-dev-11-1 cuda-driver-dev-11-1 cuda-gdb-11-1 cuda-memcheck-11-1
  cuda-nvcc-11-1 cuda-nvdisasm-11-1 cuda-nvprof-11-1 cuda-sanitizer-11-1 dpkg-dev g++ g++-7 gcc gcc-7 gcc-7-base git git-man hmmer kalign
  libarchive13 libasan4 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libcurl4 libdivsufsort3 libdpkg-perl
  liberror-perl libexpat1 libgcc-7-dev libgdbm-compat4 libgdbm5 libgomp1 libgssapi-krb5-2 libicu60 libisl19 libitm1 libjsoncpp1 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 liblzo2-2 libmpc3 libmpfr6 libmpx2 libnghttp2-14 libperl5.26 libpsl5 libquadmath0 librhash0
  librtmp1 libstdc++-7-dev libtsan0 libubsan0 libuv1 libxml2 linux-libc-dev make multiarch-support patch perl perl-modules-5.26 tzdata wget
  xz-utils
0 upgraded, 82 newly installed, 0 to remove and 22 not upgraded.
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Current default time zone: 'Etc/UTC'
Local time is now:      Wed Feb  8 17:25:52 UTC 2023.
Universal Time is now:  Wed Feb  8 17:25:52 UTC 2023.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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Setting up cuda-command-line-tools-11-1 (11.1.1-1) ...
Processing triggers for libc-bin (2.27-3ubuntu1.6) ...
+ rm -rf /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-backports_InRelease /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-backports_main_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-backports_universe_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-updates_InRelease /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-updates_main_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-updates_multiverse_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-updates_restricted_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic-updates_universe_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic_InRelease /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic_main_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic_multiverse_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic_restricted_binary-amd64_Packages.lz4 /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_bionic_universe_binary-amd64_Packages.lz4 /var/lib/apt/lists/auxfiles /var/lib/apt/lists/developer.download.nvidia.com_compute_cuda_repos_ubuntu1804_x86%5f64_InRelease /var/lib/apt/lists/developer.download.nvidia.com_compute_cuda_repos_ubuntu1804_x86%5f64_Packages.lz4 /var/lib/apt/lists/lock /var/lib/apt/lists/partial /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_bionic-security_InRelease /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_bionic-security_main_binary-amd64_Packages.lz4 /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_bionic-security_multiverse_binary-amd64_Packages.lz4 /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_bionic-security_restricted_binary-amd64_Packages.lz4 /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_bionic-security_universe_binary-amd64_Packages.lz4
+ apt-get autoremove -y
Reading package lists... Done
Building dependency tree       
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+ apt-get clean
+ /bin/rm -rf /tmp/hh-suite
+ git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite
Cloning into '/tmp/hh-suite'...
remote: Enumerating objects: 9214, done.
remote: Counting objects: 100% (634/634), done.
remote: Compressing objects: 100% (183/183), done.
remote: Total 9214 (delta 448), reused 622 (delta 444), pack-reused 8580
Receiving objects: 100% (9214/9214), 23.79 MiB | 39.94 MiB/s, done.
Resolving deltas: 100% (6975/6975), done.
Note: checking out '47a835a6329e8041741160c1196bc82d718d56e0'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

+ mkdir /tmp/hh-suite/build
+ cd /tmp/hh-suite/build
+ cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite ..
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Compiler is GNU 
-- Looking for fmemopen
-- Looking for fmemopen - found
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) 
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) 
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) 
-- xxd not found, using xxdi.pl instead
-- Performing Test HAVE_AVX2_EXTENSIONS
-- Performing Test HAVE_AVX2_EXTENSIONS - Success
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
-- Performing Test HAVE_SSE4_2_EXTENSIONS
-- Performing Test HAVE_SSE4_2_EXTENSIONS - Success
-- Performing Test HAVE_SSE4_1_EXTENSIONS
-- Performing Test HAVE_SSE4_1_EXTENSIONS - Success
-- Performing Test HAVE_SSE3_EXTENSIONS
-- Performing Test HAVE_SSE3_EXTENSIONS - Success
-- Performing Test HAVE_SSE2_EXTENSIONS
-- Performing Test HAVE_SSE2_EXTENSIONS - Success
-- Performing Test HAVE_SSE_EXTENSIONS
-- Performing Test HAVE_SSE_EXTENSIONS - Success
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Found OpenMP
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/hh-suite/build
+ make -j 4
Scanning dependencies of target CS_OBJECTS
Scanning dependencies of target hhviterbialgorithm_with_celloff
Scanning dependencies of target generated
Scanning dependencies of target ffindex
[  1%] Generating ../generated/context_data.crf.h
[  2%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o
[  3%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
[  4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o
[  5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o
[  6%] Linking C static library libffindex.a
[  6%] Built target ffindex
[  7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o
Scanning dependencies of target hhviterbialgorithm_and_ss
[  8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
[  9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o
[ 10%] Linking CXX static library libhhviterbialgorithm_with_celloff.a
[ 10%] Built target hhviterbialgorithm_with_celloff
Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss
[ 11%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o
[ 13%] Linking CXX static library libhhviterbialgorithm_and_ss.a
[ 13%] Built target hhviterbialgorithm_and_ss
Scanning dependencies of target A3M_COMPRESS
[ 13%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o
[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o
[ 15%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a
[ 15%] Built target hhviterbialgorithm_with_celloff_and_ss
Scanning dependencies of target ffindex_reduce
[ 16%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o
[ 17%] Linking C executable ffindex_reduce
[ 18%] Linking CXX static library libA3M_COMPRESS.a
[ 18%] Built target ffindex_reduce
[ 19%] Generating ../generated/context_data.lib.h
[ 19%] Built target A3M_COMPRESS
Scanning dependencies of target ffindex_build
Scanning dependencies of target ffindex_get
[ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o
[ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o
[ 22%] Linking C executable ffindex_get
[ 23%] Linking C executable ffindex_build
[ 23%] Built target ffindex_get
[ 23%] Built target ffindex_build
Scanning dependencies of target ffindex_from_fasta
Scanning dependencies of target ffindex_apply
[ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o
[ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o
/tmp/hh-suite/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry':
/tmp/hh-suite/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t {aka long int}' [-Wformat=]
             fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
                                                  ~~~^                                                    ~~~~~~~~~~~
                                                  %ld
[ 26%] Linking C executable ffindex_from_fasta
[ 27%] Linking C executable ffindex_apply
[ 27%] Built target ffindex_from_fasta
Scanning dependencies of target ffindex_modify
[ 28%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o
[ 28%] Built target ffindex_apply
[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o
Scanning dependencies of target ffindex_from_fasta_with_split
[ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o
[ 31%] Linking C executable ffindex_modify
[ 32%] Linking C executable ffindex_from_fasta_with_split
[ 32%] Built target ffindex_modify
Scanning dependencies of target ffindex_unpack
[ 32%] Built target ffindex_from_fasta_with_split
[ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o
Scanning dependencies of target ffindex_order
[ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o
[ 35%] Linking C executable ffindex_unpack
[ 36%] Linking C executable ffindex_order
[ 36%] Built target ffindex_unpack
[ 37%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o
Scanning dependencies of target a3m_database_extract
[ 37%] Built target ffindex_order
[ 38%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o
Scanning dependencies of target a3m_reduce
[ 39%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o
[ 40%] Linking CXX executable a3m_reduce
[ 41%] Linking CXX executable a3m_database_extract
[ 41%] Built target a3m_reduce
Scanning dependencies of target a3m_extract
[ 41%] Built target a3m_database_extract
Scanning dependencies of target a3m_database_reduce
[ 42%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o
[ 43%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o
[ 44%] Linking CXX static library libCS_OBJECTS.a
[ 44%] Built target CS_OBJECTS
Scanning dependencies of target a3m_database_filter
[ 45%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o
[ 46%] Linking CXX executable a3m_extract
[ 47%] Generating ../generated/cs219.lib.h
[ 48%] Linking CXX executable a3m_database_reduce
[ 48%] Built target generated
[ 48%] Built target a3m_extract
Scanning dependencies of target HH_OBJECTS
[ 48%] Built target a3m_database_reduce
[ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o
[ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o
[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o
[ 52%] Linking CXX executable a3m_database_filter
[ 52%] Built target a3m_database_filter
[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o
[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o
[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o
[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o
[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o
[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o
[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o
[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o
[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o
[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o
[ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o
[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o
/tmp/hh-suite/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])':
/tmp/hh-suite/src/hhalignment.cpp:1596:5: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=]
 int Alignment::Filter2(char keep[], int coverage, int qid, float qsc,
     ^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhalignment.h:6,
                 from /tmp/hh-suite/src/hhalignment.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
[ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o
[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o
[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o
[ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o
[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o
[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o
[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o
[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o
[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o
[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o
[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o
[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o
[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
[ 79%] Linking CXX static library libHH_OBJECTS.a
[ 79%] Built target HH_OBJECTS
Scanning dependencies of target hhblits_omp
Scanning dependencies of target hhsearch_omp
Scanning dependencies of target hhblits_ca3m
Scanning dependencies of target hhalign_omp
[ 80%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o
[ 81%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o
[ 82%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o
[ 83%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o
/tmp/hh-suite/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_ca3m.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhblits_ca3m.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
[ 84%] Linking CXX executable hhblits_ca3m
/tmp/hh-suite/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_omp.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhsearch.h:34,
                 from /tmp/hh-suite/src/hhblits_omp.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
/tmp/hh-suite/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_omp.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhsearch.h:34,
                 from /tmp/hh-suite/src/hhblits_omp.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
/tmp/hh-suite/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_omp.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhsearch.h:34,
                 from /tmp/hh-suite/src/hhblits_omp.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
[ 85%] Linking CXX executable hhblits_omp
[ 86%] Linking CXX executable hhalign_omp
[ 87%] Linking CXX executable hhsearch_omp
[ 87%] Built target hhblits_ca3m
Scanning dependencies of target cstranslate
[ 87%] Built target hhalign_omp
[ 87%] Built target hhblits_omp
[ 87%] Built target hhsearch_omp
Scanning dependencies of target hhsearch
Scanning dependencies of target hhalign
Scanning dependencies of target hhblits
[ 88%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o
[ 89%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o
[ 90%] Building CXX object src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o
[ 91%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o
[ 92%] Linking CXX executable hhalign
[ 93%] Linking CXX executable hhsearch
[ 94%] Linking CXX executable hhblits
[ 94%] Built target hhsearch
[ 94%] Built target hhblits
[ 94%] Built target hhalign
Scanning dependencies of target hhfilter
Scanning dependencies of target hhconsensus
Scanning dependencies of target hhmake
[ 95%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o
[ 96%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o
[ 97%] Building CXX object src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o
[ 98%] Linking CXX executable hhmake
[ 99%] Linking CXX executable hhfilter
[100%] Linking CXX executable hhconsensus
[100%] Built target hhfilter
[100%] Built target hhmake
[100%] Built target hhconsensus
[100%] Linking CXX executable cstranslate
[100%] Built target cstranslate
+ make install
[  3%] Built target ffindex
[  5%] Built target ffindex_reduce
[  7%] Built target ffindex_build
[  9%] Built target ffindex_get
[ 11%] Built target ffindex_from_fasta
[ 13%] Built target ffindex_apply
[ 15%] Built target ffindex_modify
[ 17%] Built target ffindex_from_fasta_with_split
[ 19%] Built target ffindex_unpack
[ 21%] Built target ffindex_order
[ 24%] Built target generated
[ 32%] Built target CS_OBJECTS
[ 34%] Built target hhviterbialgorithm_with_celloff
[ 36%] Built target hhviterbialgorithm_and_ss
[ 38%] Built target hhviterbialgorithm_with_celloff_and_ss
[ 68%] Built target HH_OBJECTS
[ 70%] Built target hhblits_ca3m
[ 72%] Built target hhalign_omp
[ 74%] Built target hhsearch_omp
[ 76%] Built target hhblits_omp
[ 77%] Built target A3M_COMPRESS
[ 78%] Built target cstranslate
[ 80%] Built target hhsearch
[ 82%] Built target hhalign
[ 84%] Built target hhblits
[ 86%] Built target hhmake
[ 88%] Built target hhfilter
[ 90%] Built target a3m_database_extract
[ 92%] Built target hhconsensus
[ 94%] Built target a3m_reduce
[ 96%] Built target a3m_extract
[ 98%] Built target a3m_database_reduce
[100%] Built target a3m_database_filter
Install the project...
-- Install configuration: "Release"
-- Installing: /opt/hhsuite/bin/ffindex_reduce
-- Installing: /opt/hhsuite/bin/ffindex_apply
-- Installing: /opt/hhsuite/bin/ffindex_build
-- Installing: /opt/hhsuite/bin/ffindex_from_fasta
-- Installing: /opt/hhsuite/bin/ffindex_get
-- Installing: /opt/hhsuite/bin/ffindex_modify
-- Installing: /opt/hhsuite/bin/ffindex_unpack
-- Installing: /opt/hhsuite/bin/ffindex_order
-- Installing: /opt/hhsuite/bin/ffindex_from_fasta_with_split
-- Installing: /opt/hhsuite/data/context_data.crf
-- Installing: /opt/hhsuite/data/context_data.lib
-- Installing: /opt/hhsuite/data/cs219.lib
-- Installing: /opt/hhsuite/data/do_not_delete
-- Installing: /opt/hhsuite/data/do_not_delete.phr
-- Installing: /opt/hhsuite/data/do_not_delete.pin
-- Installing: /opt/hhsuite/data/do_not_delete.psq
-- Installing: /opt/hhsuite/bin/hhblits
-- Installing: /opt/hhsuite/bin/hhmake
-- Installing: /opt/hhsuite/bin/hhfilter
-- Installing: /opt/hhsuite/bin/hhsearch
-- Installing: /opt/hhsuite/bin/hhalign
-- Installing: /opt/hhsuite/bin/hhconsensus
-- Installing: /opt/hhsuite/bin/a3m_extract
-- Installing: /opt/hhsuite/bin/a3m_reduce
-- Installing: /opt/hhsuite/bin/a3m_database_reduce
-- Installing: /opt/hhsuite/bin/a3m_database_extract
-- Installing: /opt/hhsuite/bin/a3m_database_filter
-- Installing: /opt/hhsuite/bin/cstranslate
-- Installing: /opt/hhsuite/bin/hhblits_omp
-- Installing: /opt/hhsuite/bin/hhsearch_omp
-- Installing: /opt/hhsuite/bin/hhalign_omp
-- Installing: /opt/hhsuite/bin/hhblits_ca3m
-- Installing: /opt/hhsuite/scripts/a3m.py
-- Installing: /opt/hhsuite/scripts/addss.pl
-- Installing: /opt/hhsuite/scripts/Align.pm
-- Installing: /opt/hhsuite/scripts/check_a3m.py
-- Installing: /opt/hhsuite/scripts/cif2fasta.py
-- Installing: /opt/hhsuite/scripts/create_profile_from_hhm.pl
-- Installing: /opt/hhsuite/scripts/create_profile_from_hmmer.pl
-- Installing: /opt/hhsuite/scripts/ffindex.py
-- Installing: /opt/hhsuite/scripts/get_a3m_size.py
-- Installing: /opt/hhsuite/scripts/hh_reader.py
-- Installing: /opt/hhsuite/scripts/hhmakemodel.pl
-- Installing: /opt/hhsuite/scripts/hhmakemodel.py
-- Installing: /opt/hhsuite/scripts/HHPaths.pm
-- Installing: /opt/hhsuite/scripts/hhsuitedb.py
-- Installing: /opt/hhsuite/scripts/mergeali.pl
-- Installing: /opt/hhsuite/scripts/multithread.pl
-- Installing: /opt/hhsuite/scripts/pdb2fasta.pl
-- Installing: /opt/hhsuite/scripts/pdbfilter.pl
-- Installing: /opt/hhsuite/scripts/pdbfilter.py
-- Installing: /opt/hhsuite/scripts/reformat.pl
-- Installing: /opt/hhsuite/scripts/renumberpdb.pl
-- Installing: /opt/hhsuite/scripts/splitfasta.pl
+ ln -s /opt/hhsuite/bin/a3m_database_extract /opt/hhsuite/bin/a3m_database_filter /opt/hhsuite/bin/a3m_database_reduce /opt/hhsuite/bin/a3m_extract /opt/hhsuite/bin/a3m_reduce /opt/hhsuite/bin/cstranslate /opt/hhsuite/bin/ffindex_apply /opt/hhsuite/bin/ffindex_build /opt/hhsuite/bin/ffindex_from_fasta /opt/hhsuite/bin/ffindex_from_fasta_with_split /opt/hhsuite/bin/ffindex_get /opt/hhsuite/bin/ffindex_modify /opt/hhsuite/bin/ffindex_order /opt/hhsuite/bin/ffindex_reduce /opt/hhsuite/bin/ffindex_unpack /opt/hhsuite/bin/hhalign /opt/hhsuite/bin/hhalign_omp /opt/hhsuite/bin/hhblits /opt/hhsuite/bin/hhblits_ca3m /opt/hhsuite/bin/hhblits_omp /opt/hhsuite/bin/hhconsensus /opt/hhsuite/bin/hhfilter /opt/hhsuite/bin/hhmake /opt/hhsuite/bin/hhsearch /opt/hhsuite/bin/hhsearch_omp /usr/bin
+ cd /
+ /bin/rm -rf /tmp/hh-suite
+ wget -q -P /tmp https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh
+ bash /tmp/Miniconda3-py37_4.12.0-Linux-x86_64.sh -b -p /opt/conda
PREFIX=/opt/conda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                                                         
Solving environment: done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py37h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py37h06a4308_2
    - cffi==1.15.0=py37hd667e15_1
    - charset-normalizer==2.0.4=pyhd3eb1b0_0
    - colorama==0.4.4=pyhd3eb1b0_0
    - conda-content-trust==0.1.1=pyhd3eb1b0_0
    - conda-package-handling==1.8.1=py37h7f8727e_0
    - conda==4.12.0=py37h06a4308_0
    - cryptography==36.0.0=py37h9ce1e76_0
    - idna==3.3=pyhd3eb1b0_0
    - ld_impl_linux-64==2.35.1=h7274673_9
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.3.0=h5101ec6_17
    - libgomp==9.3.0=h5101ec6_17
    - libstdcxx-ng==9.3.0=hd4cf53a_17
    - ncurses==6.3=h7f8727e_2
    - openssl==1.1.1n=h7f8727e_0
    - pip==21.2.2=py37h06a4308_0
    - pycosat==0.6.3=py37h27cfd23_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py37_1
    - python==3.7.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py37h27cfd23_0
    - setuptools==61.2.0=py37h06a4308_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=hc218d9a_0
    - tk==8.6.11=h1ccaba5_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.12=h7f8727e_1

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py37h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py37hd667e15_1
  charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
  colorama           pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
  conda              pkgs/main/linux-64::conda-4.12.0-py37h06a4308_0
  conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py37h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py37h9ce1e76_0
  idna               pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openssl            pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h27cfd23_0
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
  pyopenssl          pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_1
  python             pkgs/main/linux-64::python-3.7.13-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py37h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py37h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1

Preparing transaction: done
Executing transaction: done
installation finished.
+ rm /tmp/Miniconda3-py37_4.12.0-Linux-x86_64.sh
+ PATH=/opt/conda/bin:/usr/local/cuda-11.1/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ conda install -qy conda==4.13.0
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - conda==4.13.0

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2023.01.10 |       h06a4308_0         120 KB
    certifi-2022.12.7          |   py37h06a4308_0         150 KB
    conda-4.13.0               |   py37h06a4308_0         890 KB
    openssl-1.1.1s             |       h7f8727e_0         3.6 MB
    ------------------------------------------------------------
                                           Total:         4.7 MB

The following packages will be UPDATED:

  ca-certificates                      2022.3.29-h06a4308_1 --> 2023.01.10-h06a4308_0
  certifi                          2021.10.8-py37h06a4308_2 --> 2022.12.7-py37h06a4308_0
  conda                               4.12.0-py37h06a4308_0 --> 4.13.0-py37h06a4308_0
  openssl                                 1.1.1n-h7f8727e_0 --> 1.1.1s-h7f8727e_0

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ conda install -y -c conda-forge openmm=7.5.1 cudatoolkit==11.1.1 pdbfixer pip python=3.7
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.13.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - cudatoolkit==11.1.1
    - openmm=7.5.1
    - pdbfixer
    - pip
    - python=3.7

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.12.7  |       ha878542_0         143 KB  conda-forge
    certifi-2022.12.7          |     pyhd8ed1ab_0         147 KB  conda-forge
    conda-22.9.0               |   py37h89c1867_1         960 KB  conda-forge
    cudatoolkit-11.1.1         |       h6406543_8        1.20 GB  conda-forge
    fftw-3.3.9                 |nompi_h74d3f13_101         6.4 MB  conda-forge
    libblas-3.9.0              |11_linux64_openblas          12 KB  conda-forge
    libcblas-3.9.0             |11_linux64_openblas          11 KB  conda-forge
    libgfortran-ng-12.2.0      |      h69a702a_19          22 KB  conda-forge
    libgfortran5-12.2.0        |      h337968e_19         1.8 MB  conda-forge
    liblapack-3.9.0            |11_linux64_openblas          11 KB  conda-forge
    libopenblas-0.3.17         |pthreads_h8fe5266_1         9.2 MB  conda-forge
    numpy-1.21.1               |   py37h038b26d_0         6.1 MB  conda-forge
    ocl-icd-2.3.0              |       h7f98852_0         118 KB  conda-forge
    ocl-icd-system-1.0.0       |                1           4 KB  conda-forge
    openmm-7.5.1               |   py37h729b507_1        10.7 MB  conda-forge
    openssl-1.1.1k             |       h7f98852_0         2.1 MB  conda-forge
    pdbfixer-1.7               |     pyhd3deb0d_0         167 KB  conda-forge
    pip-23.0                   |     pyhd8ed1ab_0         1.3 MB  conda-forge
    python-3.7.10              |hffdb5ce_100_cpython        57.3 MB  conda-forge
    python_abi-3.7             |          3_cp37m           6 KB  conda-forge
    toolz-0.12.0               |     pyhd8ed1ab_0          48 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        1.30 GB

The following NEW packages will be INSTALLED:

  cudatoolkit        conda-forge/linux-64::cudatoolkit-11.1.1-h6406543_8
  fftw               conda-forge/linux-64::fftw-3.3.9-nompi_h74d3f13_101
  libblas            conda-forge/linux-64::libblas-3.9.0-11_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-11_linux64_openblas
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19
  libgfortran5       conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19
  liblapack          conda-forge/linux-64::liblapack-3.9.0-11_linux64_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.17-pthreads_h8fe5266_1
  numpy              conda-forge/linux-64::numpy-1.21.1-py37h038b26d_0
  ocl-icd            conda-forge/linux-64::ocl-icd-2.3.0-h7f98852_0
  ocl-icd-system     conda-forge/linux-64::ocl-icd-system-1.0.0-1
  openmm             conda-forge/linux-64::openmm-7.5.1-py37h729b507_1
  pdbfixer           conda-forge/noarch::pdbfixer-1.7-pyhd3deb0d_0
  python_abi         conda-forge/linux-64::python_abi-3.7-3_cp37m
  toolz              conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0

The following packages will be UPDATED:

  conda              pkgs/main::conda-4.13.0-py37h06a4308_0 --> conda-forge::conda-22.9.0-py37h89c1867_1
  pip                pkgs/main/linux-64::pip-21.2.2-py37h0~ --> conda-forge/noarch::pip-23.0-pyhd8ed1ab_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-ha878542_0
  certifi            pkgs/main/linux-64::certifi-2022.12.7~ --> conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0
  openssl              pkgs/main::openssl-1.1.1s-h7f8727e_0 --> conda-forge::openssl-1.1.1k-h7f98852_0
  python                pkgs/main::python-3.7.13-h12debd9_0 --> conda-forge::python-3.7.10-hffdb5ce_100_cpython

Downloading and Extracting Packages
toolz-0.12.0         | 48 KB     | ####################################################################################################### | 100% 
ca-certificates-2022 | 143 KB    | ####################################################################################################### | 100% 
openssl-1.1.1k       | 2.1 MB    | ####################################################################################################### | 100% 
fftw-3.3.9           | 6.4 MB    | ####################################################################################################### | 100% 
python-3.7.10        | 57.3 MB   | ####################################################################################################### | 100% 
libopenblas-0.3.17   | 9.2 MB    | ####################################################################################################### | 100% 
conda-22.9.0         | 960 KB    | ####################################################################################################### | 100% 
numpy-1.21.1         | 6.1 MB    | ####################################################################################################### | 100% 
liblapack-3.9.0      | 11 KB     | ####################################################################################################### | 100% 
ocl-icd-2.3.0        | 118 KB    | ####################################################################################################### | 100% 
libgfortran-ng-12.2. | 22 KB     | ####################################################################################################### | 100% 
pip-23.0             | 1.3 MB    | ####################################################################################################### | 100% 
libgfortran5-12.2.0  | 1.8 MB    | ####################################################################################################### | 100% 
python_abi-3.7       | 6 KB      | ####################################################################################################### | 100% 
libblas-3.9.0        | 12 KB     | ####################################################################################################### | 100% 
pdbfixer-1.7         | 167 KB    | ####################################################################################################### | 100% 
certifi-2022.12.7    | 147 KB    | ####################################################################################################### | 100% 
cudatoolkit-11.1.1   | 1.20 GB   | ####################################################################################################### | 100% 
openmm-7.5.1         | 10.7 MB   | ####################################################################################################### | 100% 
libcblas-3.9.0       | 11 KB     | ####################################################################################################### | 100% 
ocl-icd-system-1.0.0 | 4 KB      | ####################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: \ By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html

done
+ conda clean --all --force-pkgs-dirs --yes
Will remove 1 package cache(s).
+ wget -q -P /app/alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
+ pip3 install --upgrade pip --no-cache-dir
Requirement already satisfied: pip in /opt/conda/lib/python3.7/site-packages (23.0)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
+ pip3 install -r /app/alphafold/requirements.txt --no-cache-dir
ERROR: Could not open requirements file: [Errno 2] No such file or directory: '/app/alphafold/requirements.txt'
+ cd /opt/conda/lib/python3.7/site-packages
/.post.script: 75: /.post.script: cannot open /app/alphafold/docker/openmm.patch: No such file
+ patch -p0
FATAL:   While performing build: while running engine: exit status 2

[prehensilecode]

Not sure. I built with Singularity 3.8.7. The build process consumed about 15 GB of space. I would make sure to have at least 32 GB. You can also try monitoring space in your tmp directory while the build runs, i.e. periodically do a df.

The error messages are coming from "inside" the container. The pip and conda in the build messages are all from "inside" the container, and have nothing to do with whatever Python/Anaconda you may have installed in the host.

[SomePersonSomeWhereInTheWorld]

Not sure. I built with Singularity 3.8.7. The build process consumed about 15 GB of space. I would make sure to have at least 32 GB. You can also try monitoring space in your tmp directory while the build runs, i.e. periodically do a df.

plenty of space in /local: /dev/sda6 407G 2.9G 405G 1% /local

Is there any debugging I can enable?

The error messages are coming from "inside" the container. The pip and conda in the build messages are all from "inside" the container, and have nothing to do with whatever Python/Anaconda you may have installed in the host.

yes I realized that after submitting the issue.

[prehensilecode]

Are you doing the build in the correct directory?

Lines 5 and 6 in the Singularity.def file copies the appropriate files into the container:

%files
. /app/alphafold

If you ran singularity build ... in the wrong place, the necessary files would not end up in /app/alphafold in the container.

You have to do these two steps in order, after downloading AlphaFold 2.2.4:

$ cd alphafold-v2.2.4
$ git clone https://github.com/prehensilecode/alphafold_singularity singularity

Instead of the git clone of the main branch, you can try cloning the tagged release:

git clone --depth 1 --branch v2.2.4 https://github.com/prehensilecode/alphafold_singularity singularity

The missing requirements.txt file is actually the main requirements.txt from the AlphaFold repository: https://github.com/deepmind/alphafold/blob/main/requirements.txt

[SomePersonSomeWhereInTheWorld]

You have to do these two steps in order, after downloading AlphaFold 2.2.4

By downloading you do mean git clone, correct? Here are the same errors on another server, RHEL 7, Singularity 3.5.3

+ wget -q -P /app/alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
+ pip3 install --upgrade pip --no-cache-dir
Requirement already satisfied: pip in /opt/conda/lib/python3.7/site-packages (23.0)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
+ pip3 install -r /app/alphafold/requirements.txt --no-cache-dir
ERROR: Could not open requirements file: [Errno 2] No such file or directory: '/app/alphafold/requirements.txt'
+ cd /opt/conda/lib/python3.7/site-packages
/.build-script-post: 75: /.build-script-post: cannot open /app/alphafold/docker/openmm.patch: No such file
+ patch -p0
FATAL:   failed to execute %post proc: exit status 2
FATAL:   While performing build: while running engine: while running /path/to/singularity-3.5.3/libexec/singularity/bin/starter: exit status 255
[me@server alphafold-v2.2.4]$ pwd
/path/to/my/home/alphafold-v2.2.4
[me@server alphafold-v2.2.4]$ ls -l
total 0
drwxr-xr-x 3 rk3199 user 4096 Feb  8 17:12 singularity
[me@server alphafold-v2.2.4]$ ls -l singularity/
total 128
-rw-r--r-- 1 me user  1334 Feb  8 17:12 example_slurm_job.sh
-rw-r--r-- 1 me user 11357 Feb  8 17:12 LICENSE
-rw-r--r-- 1 me user  2015 Feb  8 17:12 README.md
-rw-r--r-- 1 me user    87 Feb  8 17:12 requirements.txt
-rw-r--r-- 1 me user 10504 Feb  8 17:12 run_singularity.py
-rw-r--r-- 1 me user  3004 Feb  8 17:12 Singularity.def

[prehensilecode]

You have to do these two steps in order, after downloading AlphaFold 2.2.4

By downloading you do mean git clone, correct? Here are the same errors on another server, RHEL 7, Singularity 3.5.3

I would download the AlphaFold release tarball, rather than cloning main. So:

$ wget https://github.com/deepmind/alphafold/archive/refs/tags/v2.2.4.tar.gz -O alphafold-2.2.4.tar.gz
--2023-02-08 17:28:45--  https://github.com/deepmind/alphafold/archive/refs/tags/v2.2.4.tar.gz
Resolving github.com (github.com)... 140.82.112.3
Connecting to github.com (github.com)|140.82.112.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/deepmind/alphafold/tar.gz/refs/tags/v2.2.4 [following]
--2023-02-08 17:28:45--  https://codeload.github.com/deepmind/alphafold/tar.gz/refs/tags/v2.2.4
Resolving codeload.github.com (codeload.github.com)... 140.82.112.9
Connecting to codeload.github.com (codeload.github.com)|140.82.112.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘alphafold-2.2.4.tar.gz’
...
2023-02-08 17:28:50 (1.24 MB/s) - ‘alphafold-2.2.4.tar.gz’ saved [5855095]
$ tar -xvf alphafold-2.2.4.tar.gz
$ cd alphafold-2.2.4
$ wget https://github.com/prehensilecode/alphafold_singularity/archive/refs/tags/v2.2.4.tar.gz -O alphafold_singularity-2.2.4.tar.gz
--2023-02-08 17:42:17--  https://github.com/prehensilecode/alphafold_singularity/archive/refs/tags/v2.2.4.tar.gz
Resolving github.com (github.com)... 140.82.113.4
Connecting to github.com (github.com)|140.82.113.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/prehensilecode/alphafold_singularity/tar.gz/refs/tags/v2.2.4 [following]
--2023-02-08 17:42:17--  https://codeload.github.com/prehensilecode/alphafold_singularity/tar.gz/refs/tags/v2.2.4
...
2023-02-08 17:42:18 (1.58 MB/s) - ‘alphafold_singularity-2.2.4.tar.gz’ saved [10148]
$ tar -xf alphafold_singularity-2.2.4.tar.gz
$ mv alphafold_singularity-2.2.4 singularity
$ python3 -m pip install -r singularity/requirements.txt
$ sudo singularity build alphafold.sif singularity/Singularity.def

[SomePersonSomeWhereInTheWorld]

Bingo that worked:

INFO:    Adding environment to container
INFO:    Adding runscript
INFO:    Creating SIF file...
INFO:    Build complete: alphafold.sif

Are there any docs on how to use the sif file with singularity commands?

[prehensilecode]

Are there any docs on how to use the sif file with singularity commands?

https://docs.sylabs.io/guides/3.5/user-guide/quick_start.html#running-a-container

[SomePersonSomeWhereInTheWorld]

Are there any docs on how to use the sif file with singularity commands?

https://docs.sylabs.io/guides/3.5/user-guide/quick_start.html#running-a-container

Well yes I know that I meant specific to the newly created sif file to access Alpha Fold related features.

[SomePersonSomeWhereInTheWorld]

From the example Slurm batch file, how is it expected to run module load alphafold/2.2.4, if it's in a Singularity container?

I pulled out the Python command and it errors out withError for command "run": unknown flag: --env

python3 /path/to/me/alphafold-2.2.4/singularity/run_singularity.py   --data_dir=/path/to/me//alphafold-dbs     --fasta_paths=T1050.fasta     --max_template_date=2020-05-14     --model_preset=monomer_casp14 
/path/to/me/alphafold-2.2.4/alphafold.sif
I0209 10:35:12.734251 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-2.2.4 -> /mnt/fasta_path_0
I0209 10:35:12.734435 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/uniref90 -> /mnt/uniref90_database_path
I0209 10:35:12.734484 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/mgnify -> /mnt/mgnify_database_path
I0209 10:35:12.734525 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs -> /mnt/data_dir
I0209 10:35:12.734563 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/pdb_mmcif -> /mnt/template_mmcif_dir
I0209 10:35:12.734601 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0209 10:35:12.734640 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/pdb70 -> /mnt/pdb70_database_path
I0209 10:35:12.734700 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path
I0209 10:35:12.734739 46912496400512 run_singularity.py:120] Binding /path/to/me/alphafold-dbs/bfd -> /mnt/bfd_database_path
singularity run --nv --bind /path/to/me/alphafold-2.2.4:/mnt/fasta_path_0,/path/to/me/alphafold-dbs/uniref90:/mnt/uniref90_database_path,/path/to/me/alphafold-dbs/mgnify:/mnt/mgnify_database_path,/path/to/me/alphafold-dbs:/mnt/data_dir,/path/to/me/alphafold-dbs/pdb_mmcif:/mnt/template_mmcif_dir,/path/to/me/alphafold-dbs/pdb_mmcif:/mnt/obsolete_pdbs_path,/path/to/me/alphafold-dbs/pdb70:/mnt/pdb70_database_path,/path/to/me/alphafold-dbs/uniclust30/uniclust30_2018_08:/mnt/uniclust30_database_path,/path/to/me/alphafold-dbs/bfd:/mnt/bfd_database_path,/tmp:/mnt/output --env TF_FORCE_UNIFIED_MEMORY=1 --env XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 --env OPENMM_CPU_THREADS=12 /path/to/me/alphafold-2.2.4/alphafold.sif --fasta_paths=/mnt/fasta_path_0/T1050.fasta --uniref90_database_path=/mnt/uniref90_database_path/uniref90.fasta --mgnify_database_path=/mnt/mgnify_database_path/mgy_clusters_2018_12.fa --data_dir=/mnt/data_dir --template_mmcif_dir=/mnt/template_mmcif_dir/mmcif_files --obsolete_pdbs_path=/mnt/obsolete_pdbs_path/obsolete.dat --pdb70_database_path=/mnt/pdb70_database_path/pdb70 --uniclust30_database_path=/mnt/uniclust30_database_path/uniclust30_2018_08 --bfd_database_path=/mnt/bfd_database_path/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --output_dir=/mnt/output --max_template_date=2020-05-14 --db_preset=full_dbs --model_preset=monomer_casp14 --benchmark=False --use_precomputed_msas=False --num_multimer_predictions_per_model=5 --run_relax=True --use_gpu_relax=True --logtostderr
Error for command "run": unknown flag: --env

LMK if you want me to open a new issue for this.

[prehensilecode]

Please open a new issue for this, since it's distinct from the original issue.