Install Alphafold2 Docker Version (II)
https://github.com/deepmind/alphafold
Running AlphaFold
The simplest way to run AlphaFold is using the provided Docker script. This was tested on Google Cloud with a machine using the nvidia-gpu-cloud-image with 12 vCPUs, 85 GB of RAM, a 100 GB boot disk, the databases on an additional 3 TB disk, and an A100 GPU.
- Clone this repository and
cdinto it.
(base) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO$ git clone https://github.com/deepmind/alphafold.git
Cloning into 'alphafold'...
remote: Enumerating objects: 569, done.
remote: Counting objects: 100% (220/220), done.
remote: Compressing objects: 100% (55/55), done.
remote: Total 569 (delta 177), reused 167 (delta 164), pack-reused 349
Receiving objects: 100% (569/569), 5.77 MiB | 26.00 KiB/s, done.
Resolving deltas: 100% (342/342), done.
(base) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO$ cd alphafold/
- Build the Docker image:
(base) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ docker build -f docker/Dockerfile -t alphafold .
Sending build context to Docker daemon 13.36MB
Step 1/18 : ARG CUDA=11.1.1
Step 2/18 : FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu18.04
11.1.1-cudnn8-runtime-ubuntu18.04: Pulling from nvidia/cuda
40dd5be53814: Pull complete
b6f8396e6f3c: Pull complete
3c444d3bc7b1: Pull complete
4b27d231d2cd: Pull complete
035911917ab7: Pull complete
d2cd37fe954b: Pull complete
6f16144b6364: Pull complete
ddab44155817: Pull complete
Digest: sha256:996e500db01edfaa1c87f5772b367896e1b87dba556279756b086250be2c1ae1
Status: Downloaded newer image for nvidia/cuda:11.1.1-cudnn8-runtime-ubuntu18.04
---> a6b5e71b6a39
Step 3/18 : ARG CUDA
---> Running in 3045c3475d2f
Removing intermediate container 3045c3475d2f
---> a7e2aecccd6e
Step 4/18 : SHELL ["/bin/bash", "-c"]
---> Running in debbf0845855
Removing intermediate container debbf0845855
---> 653d7c438d50
Step 5/18 : RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential cmake cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) git hmmer kalign tzdata wget && rm -rf /var/lib/apt/lists/*
---> Running in 0edc9dc291c4
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Fetched 26.8 MB in 15s (1821 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
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 fakeroot
g++ g++-7 gcc gcc-7 gcc-7-base git-man krb5-locales less
libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl
libarchive13 libasan4 libatomic1 libbinutils libbsd0 libc-dev-bin libc6
libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libcurl4 libdivsufsort3
libdpkg-perl libedit2 liberror-perl libexpat1 libfakeroot
libfile-fcntllock-perl libgcc-7-dev libgdbm-compat4 libgdbm5 libgomp1
libgssapi-krb5-2 libicu60 libisl19 libitm1 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0
liblzo2-2 libmpc3 libmpfr6 libmpx2 libnghttp2-14 libperl5.26 libpsl5
libquadmath0 librhash0 librtmp1 libssl1.0.0 libstdc++-7-dev libtsan0
libubsan0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6
libxml2 libxmuu1 linux-libc-dev make manpages manpages-dev multiarch-support
netbase openssh-client patch perl perl-modules-5.26 publicsuffix xauth
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 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
locales bzr gdbm-l10n krb5-doc krb5-user libstdc++-7-doc make-doc
man-browser keychain libpam-ssh monkeysphere ssh-askpass ed diffutils-doc
perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl
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 fakeroot g++ g++-7 gcc gcc-7
gcc-7-base git git-man hmmer kalign krb5-locales less libalgorithm-diff-perl
libalgorithm-diff-xs-perl libalgorithm-merge-perl libarchive13 libasan4
libatomic1 libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0 libcilkrts5
libcurl3-gnutls libcurl4 libdivsufsort3 libdpkg-perl libedit2 liberror-perl
libexpat1 libfakeroot libfile-fcntllock-perl libgcc-7-dev libgdbm-compat4
libgdbm5 libgomp1 libgssapi-krb5-2 libicu60 libisl19 libitm1 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl
liblsan0 liblzo2-2 libmpc3 libmpfr6 libmpx2 libnghttp2-14 libperl5.26
libpsl5 libquadmath0 librhash0 librtmp1 libssl1.0.0 libstdc++-7-dev libtsan0
libubsan0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6
libxml2 libxmuu1 linux-libc-dev make manpages manpages-dev multiarch-support
netbase openssh-client patch perl perl-modules-5.26 publicsuffix tzdata wget
xauth xz-utils
The following packages will be upgraded:
libc6
1 upgraded, 107 newly installed, 0 to remove and 28 not upgraded.
Need to get 166 MB of archives.
After this operation, 599 MB of additional disk space will be used.
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debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 4832 files and directories currently installed.)
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Removing intermediate container 0edc9dc291c4
---> 5435c388f720
Step 6/18 : RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite && mkdir /tmp/hh-suite/build && pushd /tmp/hh-suite/build && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. && make -j 4 && make install && ln -s /opt/hhsuite/bin/* /usr/bin && popd && rm -rf /tmp/hh-suite
---> Running in 7d0f5549d48a
Cloning into '/tmp/hh-suite'...
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>
/tmp/hh-suite/build /
-- 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
Scanning dependencies of target generated
Scanning dependencies of target ffindex
Scanning dependencies of target CS_OBJECTS
[ 1%] Generating ../generated/context_data.crf.h
[ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o
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[ 3%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o
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[ 19%] Built target hhviterbialgorithm_with_celloff_and_ss
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[ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.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
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[ 51%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o
[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o
[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o
[ 54%] Linking CXX executable a3m_database_filter
[ 54%] Built target a3m_database_filter
[ 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
/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 ());
^
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o
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[ 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_ca3m
Scanning dependencies of target hhsearch_omp
Scanning dependencies of target hhalign_omp
Scanning dependencies of target hhblits_omp
[ 80%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o
[ 81%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o
[ 82%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o
[ 83%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.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
[ 87%] Built target hhalign_omp
[ 87%] Built target hhblits_omp
[ 87%] Built target hhsearch_omp
Scanning dependencies of target cstranslate
Scanning dependencies of target hhalign
[ 88%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o
Scanning dependencies of target hhsearch
[ 89%] Building CXX object src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o
Scanning dependencies of target hhblits
[ 90%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o
[ 91%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o
[ 92%] Linking CXX executable hhblits
[ 93%] Linking CXX executable hhsearch
[ 94%] Linking CXX executable hhalign
[ 94%] Built target hhblits
Scanning dependencies of target hhmake
[ 94%] Built target hhsearch
[ 95%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o
[ 95%] Built target hhalign
Scanning dependencies of target hhfilter
[ 96%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o
Scanning dependencies of target hhconsensus
[ 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 hhmake
[100%] Built target hhfilter
[100%] Built target hhconsensus
[100%] Linking CXX executable cstranslate
[100%] Built target cstranslate
[ 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
/
Removing intermediate container 7d0f5549d48a
---> 69f17acd3345
Step 7/18 : RUN wget -q -P /tmp https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
---> Running in 00cf5eeab640
PREFIX=/opt/conda
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... 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=py39h27cfd23_1003
- ca-certificates==2022.3.29=h06a4308_1
- certifi==2021.10.8=py39h06a4308_2
- cffi==1.15.0=py39hd667e15_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=py39h7f8727e_0
- conda==4.12.0=py39h06a4308_0
- cryptography==36.0.0=py39h9ce1e76_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==21.2.4=py39h06a4308_0
- pycosat==0.6.3=py39h27cfd23_0
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py39h06a4308_0
- python==3.9.12=h12debd9_0
- readline==8.1.2=h7f8727e_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py39h27cfd23_0
- setuptools==61.2.0=py39h06a4308_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
- tzdata==2022a=hda174b7_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-py39h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
certifi pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2
cffi pkgs/main/linux-64::cffi-1.15.0-py39hd667e15_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-py39h06a4308_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-py39h7f8727e_0
cryptography pkgs/main/linux-64::cryptography-36.0.0-py39h9ce1e76_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-21.2.4-py39h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_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-py39h06a4308_0
python pkgs/main/linux-64::python-3.9.12-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-py39h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-61.2.0-py39h06a4308_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
tzdata pkgs/main/noarch::tzdata-2022a-hda174b7_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: ...working... done
Executing transaction: ...working... done
installation finished.
Removing intermediate container 00cf5eeab640
---> 6da2c0e72429
Step 8/18 : ENV PATH="/opt/conda/bin:$PATH"
---> Running in 7c44adc6e4ac
Removing intermediate container 7c44adc6e4ac
---> 579e466e2f09
Step 9/18 : RUN conda update -qy conda && conda install -y -c conda-forge openmm=7.5.1 cudatoolkit==${CUDA_VERSION} pdbfixer pip python=3.7
---> Running in b479fe3ee749
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /opt/conda
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
_openmp_mutex-5.1 | 1_gnu 21 KB
ca-certificates-2022.07.19 | h06a4308_0 124 KB
certifi-2022.6.15 | py39h06a4308_0 153 KB
cffi-1.15.1 | py39h74dc2b5_0 228 KB
conda-4.13.0 | py39h06a4308_0 895 KB
cryptography-37.0.1 | py39h9ce1e76_0 1.3 MB
ld_impl_linux-64-2.38 | h1181459_1 654 KB
libgcc-ng-11.2.0 | h1234567_1 5.3 MB
libgomp-11.2.0 | h1234567_1 474 KB
libstdcxx-ng-11.2.0 | h1234567_1 4.7 MB
ncurses-6.3 | h5eee18b_3 781 KB
openssl-1.1.1q | h7f8727e_0 2.5 MB
pip-22.1.2 | py39h06a4308_0 2.5 MB
requests-2.28.1 | py39h06a4308_0 92 KB
sqlite-3.39.2 | h5082296_0 1.1 MB
tk-8.6.12 | h1ccaba5_0 3.0 MB
tqdm-4.64.0 | py39h06a4308_0 126 KB
urllib3-1.26.11 | py39h06a4308_0 182 KB
xz-5.2.5 | h7f8727e_1 339 KB
zlib-1.2.12 | h7f8727e_2 106 KB
------------------------------------------------------------
Total: 24.5 MB
The following packages will be REMOVED:
colorama-0.4.4-pyhd3eb1b0_0
conda-content-trust-0.1.1-pyhd3eb1b0_0
six-1.16.0-pyhd3eb1b0_1
The following packages will be UPDATED:
_openmp_mutex 4.5-1_gnu --> 5.1-1_gnu
ca-certificates 2022.3.29-h06a4308_1 --> 2022.07.19-h06a4308_0
certifi 2021.10.8-py39h06a4308_2 --> 2022.6.15-py39h06a4308_0
cffi 1.15.0-py39hd667e15_1 --> 1.15.1-py39h74dc2b5_0
conda 4.12.0-py39h06a4308_0 --> 4.13.0-py39h06a4308_0
cryptography 36.0.0-py39h9ce1e76_0 --> 37.0.1-py39h9ce1e76_0
ld_impl_linux-64 2.35.1-h7274673_9 --> 2.38-h1181459_1
libgcc-ng 9.3.0-h5101ec6_17 --> 11.2.0-h1234567_1
libgomp 9.3.0-h5101ec6_17 --> 11.2.0-h1234567_1
libstdcxx-ng 9.3.0-hd4cf53a_17 --> 11.2.0-h1234567_1
ncurses 6.3-h7f8727e_2 --> 6.3-h5eee18b_3
openssl 1.1.1n-h7f8727e_0 --> 1.1.1q-h7f8727e_0
pip 21.2.4-py39h06a4308_0 --> 22.1.2-py39h06a4308_0
requests pkgs/main/noarch::requests-2.27.1-pyh~ --> pkgs/main/linux-64::requests-2.28.1-py39h06a4308_0
sqlite 3.38.2-hc218d9a_0 --> 3.39.2-h5082296_0
tk 8.6.11-h1ccaba5_0 --> 8.6.12-h1ccaba5_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb~ --> pkgs/main/linux-64::tqdm-4.64.0-py39h06a4308_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd~ --> pkgs/main/linux-64::urllib3-1.26.11-py39h06a4308_0
xz 5.2.5-h7b6447c_0 --> 5.2.5-h7f8727e_1
zlib 1.2.12-h7f8727e_1 --> 1.2.12-h7f8727e_2
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## 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-2022.6.15 | ha878542_0 149 KB conda-forge
certifi-2022.6.15 | py37h89c1867_0 155 KB conda-forge
cffi-1.14.6 | py37hc58025e_0 225 KB conda-forge
colorama-0.4.5 | pyhd8ed1ab_0 18 KB conda-forge
conda-4.14.0 | py37h89c1867_0 1010 KB conda-forge
conda-package-handling-1.8.1| py37h540881e_1 1.0 MB conda-forge
cryptography-37.0.2 | py37h38fbfac_0 1.5 MB conda-forge
cudatoolkit-11.1.1 | ha002fc5_10 1.20 GB conda-forge
fftw-3.3.10 |nompi_h77c792f_102 6.4 MB conda-forge
libblas-3.9.0 |15_linux64_openblas 12 KB conda-forge
libcblas-3.9.0 |15_linux64_openblas 12 KB conda-forge
libgfortran-ng-12.1.0 | h69a702a_16 23 KB conda-forge
libgfortran5-12.1.0 | hdcd56e2_16 1.8 MB conda-forge
liblapack-3.9.0 |15_linux64_openblas 12 KB conda-forge
libopenblas-0.3.20 |pthreads_h78a6416_0 10.1 MB conda-forge
numpy-1.21.6 | py37h976b520_0 6.1 MB conda-forge
ocl-icd-2.3.1 | h7f98852_0 119 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-1.1.1o | h166bdaf_0 2.1 MB conda-forge
pdbfixer-1.7 | pyhd3deb0d_0 167 KB conda-forge
pip-22.2.2 | pyhd8ed1ab_0 1.5 MB conda-forge
pycosat-0.6.3 |py37h540881e_1010 107 KB conda-forge
pysocks-1.7.1 | py37h89c1867_5 28 KB conda-forge
python-3.7.10 |hffdb5ce_100_cpython 57.3 MB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
requests-2.28.1 | pyhd8ed1ab_0 53 KB conda-forge
ruamel_yaml-0.15.80 |py37h5e8e339_1006 270 KB conda-forge
setuptools-65.0.2 | py37h89c1867_0 1.4 MB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
toolz-0.12.0 | pyhd8ed1ab_0 48 KB conda-forge
tqdm-4.64.0 | pyhd8ed1ab_0 81 KB conda-forge
urllib3-1.25.8 | py37hc8dfbb8_1 160 KB conda-forge
------------------------------------------------------------
Total: 1.30 GB
The following NEW packages will be INSTALLED:
colorama conda-forge/noarch::colorama-0.4.5-pyhd8ed1ab_0
cudatoolkit conda-forge/linux-64::cudatoolkit-11.1.1-ha002fc5_10
fftw conda-forge/linux-64::fftw-3.3.10-nompi_h77c792f_102
libblas conda-forge/linux-64::libblas-3.9.0-15_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-15_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.1.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-12.1.0-hdcd56e2_16
liblapack conda-forge/linux-64::liblapack-3.9.0-15_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
numpy conda-forge/linux-64::numpy-1.21.6-py37h976b520_0
ocl-icd conda-forge/linux-64::ocl-icd-2.3.1-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-3.7-2_cp37m
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
toolz conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0
The following packages will be REMOVED:
brotlipy-0.7.0-py39h27cfd23_1003
The following packages will be UPDATED:
conda pkgs/main::conda-4.13.0-py39h06a4308_0 --> conda-forge::conda-4.14.0-py37h89c1867_0
conda-package-han~ pkgs/main::conda-package-handling-1.8~ --> conda-forge::conda-package-handling-1.8.1-py37h540881e_1
cryptography pkgs/main::cryptography-37.0.1-py39h9~ --> conda-forge::cryptography-37.0.2-py37h38fbfac_0
pip pkgs/main/linux-64::pip-22.1.2-py39h0~ --> conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
pycosat pkgs/main::pycosat-0.6.3-py39h27cfd23~ --> conda-forge::pycosat-0.6.3-py37h540881e_1010
pysocks pkgs/main::pysocks-1.7.1-py39h06a4308~ --> conda-forge::pysocks-1.7.1-py37h89c1867_5
setuptools pkgs/main::setuptools-61.2.0-py39h06a~ --> conda-forge::setuptools-65.0.2-py37h89c1867_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.6.15-ha878542_0
certifi pkgs/main::certifi-2022.6.15-py39h06a~ --> conda-forge::certifi-2022.6.15-py37h89c1867_0
cffi pkgs/main::cffi-1.15.1-py39h74dc2b5_0 --> conda-forge::cffi-1.14.6-py37hc58025e_0
openssl pkgs/main::openssl-1.1.1q-h7f8727e_0 --> conda-forge::openssl-1.1.1o-h166bdaf_0
python pkgs/main::python-3.9.12-h12debd9_0 --> conda-forge::python-3.7.10-hffdb5ce_100_cpython
requests pkgs/main/linux-64::requests-2.28.1-p~ --> conda-forge/noarch::requests-2.28.1-pyhd8ed1ab_0
ruamel_yaml pkgs/main::ruamel_yaml-0.15.100-py39h~ --> conda-forge::ruamel_yaml-0.15.80-py37h5e8e339_1006
tqdm pkgs/main/linux-64::tqdm-4.64.0-py39h~ --> conda-forge/noarch::tqdm-4.64.0-pyhd8ed1ab_0
urllib3 pkgs/main::urllib3-1.26.11-py39h06a43~ --> conda-forge::urllib3-1.25.8-py37hc8dfbb8_1
Downloading and Extracting Packages
cryptography-37.0.2 | 1.5 MB | ########## | 100%
libcblas-3.9.0 | 12 KB | ########## | 100%
cudatoolkit-11.1.1 | 1.20 GB | ########## | 100%
libgfortran5-12.1.0 | 1.8 MB | ########## | 100%
tqdm-4.64.0 | 81 KB | ########## | 100%
libopenblas-0.3.20 | 10.1 MB | ########## | 100%
python-3.7.10 | 57.3 MB | ########## | 100%
toolz-0.12.0 | 48 KB | ########## | 100%
ruamel_yaml-0.15.80 | 270 KB | ########## | 100%
urllib3-1.25.8 | 160 KB | ########## | 100%
pdbfixer-1.7 | 167 KB | ########## | 100%
conda-package-handli | 1.0 MB | ########## | 100%
certifi-2022.6.15 | 155 KB | ########## | 100%
colorama-0.4.5 | 18 KB | ########## | 100%
ca-certificates-2022 | 149 KB | ########## | 100%
pysocks-1.7.1 | 28 KB | ########## | 100%
ocl-icd-system-1.0.0 | 4 KB | ########## | 100%
six-1.16.0 | 14 KB | ########## | 100%
setuptools-65.0.2 | 1.4 MB | ########## | 100%
pycosat-0.6.3 | 107 KB | ########## | 100%
openmm-7.5.1 | 10.7 MB | ########## | 100%
libgfortran-ng-12.1. | 23 KB | ########## | 100%
fftw-3.3.10 | 6.4 MB | ########## | 100%
ocl-icd-2.3.1 | 119 KB | ########## | 100%
python_abi-3.7 | 4 KB | ########## | 100%
numpy-1.21.6 | 6.1 MB | ########## | 100%
cffi-1.14.6 | 225 KB | ########## | 100%
pip-22.2.2 | 1.5 MB | ########## | 100%
openssl-1.1.1o | 2.1 MB | ########## | 100%
requests-2.28.1 | 53 KB | ########## | 100%
conda-4.14.0 | 1010 KB | ########## | 100%
libblas-3.9.0 | 12 KB | ########## | 100%
liblapack-3.9.0 | 12 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... 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
Removing intermediate container b479fe3ee749
---> ca27b5a16cf6
Step 10/18 : COPY . /app/alphafold
---> 615722fdb768
Step 11/18 : RUN wget -q -P /app/alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
---> Running in 97660456ed02
Removing intermediate container 97660456ed02
---> 4ed31478dec1
Step 12/18 : RUN pip3 install --upgrade pip && pip3 install -r /app/alphafold/requirements.txt && pip3 install --upgrade jax==0.2.14 jaxlib==0.1.69+cuda$(cut -f1,2 -d. <<< ${CUDA} | sed 's/\.//g') -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
---> Running in f99f777d4868
Requirement already satisfied: pip in /opt/conda/lib/python3.7/site-packages (22.2.2)
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
Collecting absl-py==0.13.0
Downloading absl_py-0.13.0-py3-none-any.whl (132 kB)
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Collecting biopython==1.79
Downloading biopython-1.79-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (2.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 6.3 MB/s eta 0:00:00
Collecting chex==0.0.7
Downloading chex-0.0.7-py3-none-any.whl (52 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.5/52.5 kB 1.5 MB/s eta 0:00:00
Collecting dm-haiku==0.0.4
Downloading dm_haiku-0.0.4-py3-none-any.whl (284 kB)
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Collecting dm-tree==0.1.6
Downloading dm_tree-0.1.6-cp37-cp37m-manylinux_2_24_x86_64.whl (93 kB)
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Collecting docker==5.0.0
Downloading docker-5.0.0-py2.py3-none-any.whl (146 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.0/147.0 kB 2.5 MB/s eta 0:00:00
Collecting immutabledict==2.0.0
Downloading immutabledict-2.0.0-py3-none-any.whl (4.0 kB)
Collecting jax==0.2.14
Downloading jax-0.2.14.tar.gz (669 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 669.2/669.2 kB 7.4 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting ml-collections==0.1.0
Downloading ml_collections-0.1.0-py3-none-any.whl (88 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.7/88.7 kB 2.8 MB/s eta 0:00:00
Collecting numpy==1.19.5
Downloading numpy-1.19.5-cp37-cp37m-manylinux2010_x86_64.whl (14.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.8/14.8 MB 949.8 kB/s eta 0:00:00
Collecting pandas==1.3.4
Downloading pandas-1.3.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 2.1 MB/s eta 0:00:00
Collecting protobuf==3.20.1
Downloading protobuf-3.20.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 2.2 MB/s eta 0:00:00
Collecting scipy==1.7.0
Downloading scipy-1.7.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 28.5/28.5 MB 1.5 MB/s eta 0:00:00
Collecting tensorflow-cpu==2.5.0
Downloading tensorflow_cpu-2.5.0-cp37-cp37m-manylinux2010_x86_64.whl (168.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 168.3/168.3 MB 1.2 MB/s eta 0:00:00
Requirement already satisfied: six in /opt/conda/lib/python3.7/site-packages (from absl-py==0.13.0->-r /app/alphafold/requirements.txt (line 1)) (1.16.0)
Collecting jaxlib>=0.1.37
Downloading jaxlib-0.3.15-cp37-none-manylinux2014_x86_64.whl (72.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 72.0/72.0 MB 1.7 MB/s eta 0:00:00
Requirement already satisfied: toolz>=0.9.0 in /opt/conda/lib/python3.7/site-packages (from chex==0.0.7->-r /app/alphafold/requirements.txt (line 3)) (0.12.0)
Collecting tabulate>=0.8.9
Downloading tabulate-0.8.10-py3-none-any.whl (29 kB)
Collecting typing-extensions
Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB)
Collecting websocket-client>=0.32.0
Downloading websocket_client-1.3.3-py3-none-any.whl (54 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.3/54.3 kB 1.0 MB/s eta 0:00:00
Requirement already satisfied: requests!=2.18.0,>=2.14.2 in /opt/conda/lib/python3.7/site-packages (from docker==5.0.0->-r /app/alphafold/requirements.txt (line 6)) (2.28.1)
Collecting opt_einsum
Downloading opt_einsum-3.3.0-py3-none-any.whl (65 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.5/65.5 kB 1.1 MB/s eta 0:00:00
Collecting PyYAML
Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB)
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Collecting contextlib2
Downloading contextlib2-21.6.0-py2.py3-none-any.whl (13 kB)
Collecting pytz>=2017.3
Downloading pytz-2022.2.1-py2.py3-none-any.whl (500 kB)
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Collecting python-dateutil>=2.7.3
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
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Collecting keras-preprocessing~=1.1.2
Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.6/42.6 kB 948.4 kB/s eta 0:00:00
Collecting six
Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting tensorflow-estimator<2.6.0,>=2.5.0rc0
Downloading tensorflow_estimator-2.5.0-py2.py3-none-any.whl (462 kB)
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Collecting google-pasta~=0.2
Downloading google_pasta-0.2.0-py3-none-any.whl (57 kB)
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Collecting flatbuffers~=1.12.0
Downloading flatbuffers-1.12-py2.py3-none-any.whl (15 kB)
Collecting keras-nightly~=2.5.0.dev
Downloading keras_nightly-2.5.0.dev2021032900-py2.py3-none-any.whl (1.2 MB)
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Requirement already satisfied: wheel~=0.35 in /opt/conda/lib/python3.7/site-packages (from tensorflow-cpu==2.5.0->-r /app/alphafold/requirements.txt (line 14)) (0.37.1)
Collecting h5py~=3.1.0
Downloading h5py-3.1.0-cp37-cp37m-manylinux1_x86_64.whl (4.0 MB)
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Collecting astunparse~=1.6.3
Downloading astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting gast==0.4.0
Downloading gast-0.4.0-py3-none-any.whl (9.8 kB)
Collecting grpcio~=1.34.0
Downloading grpcio-1.34.1-cp37-cp37m-manylinux2014_x86_64.whl (4.0 MB)
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Collecting typing-extensions
Downloading typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting termcolor~=1.1.0
Downloading termcolor-1.1.0.tar.gz (3.9 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting tensorboard~=2.5
Downloading tensorboard-2.10.0-py3-none-any.whl (5.9 MB)
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Collecting wrapt~=1.12.1
Downloading wrapt-1.12.1.tar.gz (27 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting cached-property
Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 6)) (1.25.8)
Requirement already satisfied: idna<4,>=2.5 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 6)) (3.3)
Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 6)) (2022.6.15)
Requirement already satisfied: charset-normalizer<3,>=2 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 6)) (2.0.4)
Collecting werkzeug>=1.0.1
Downloading Werkzeug-2.2.2-py3-none-any.whl (232 kB)
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Collecting tensorboard-plugin-wit>=1.6.0
Downloading tensorboard_plugin_wit-1.8.1-py3-none-any.whl (781 kB)
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Collecting tensorboard~=2.5
Downloading tensorboard-2.9.1-py3-none-any.whl (5.8 MB)
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Downloading tensorboard-2.9.0-py3-none-any.whl (5.8 MB)
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Collecting google-auth<3,>=1.6.3
Downloading google_auth-2.10.0-py2.py3-none-any.whl (167 kB)
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Collecting tensorboard-data-server<0.7.0,>=0.6.0
Downloading tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB)
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Requirement already satisfied: setuptools>=41.0.0 in /opt/conda/lib/python3.7/site-packages (from tensorboard~=2.5->tensorflow-cpu==2.5.0->-r /app/alphafold/requirements.txt (line 14)) (65.0.2)
Collecting google-auth-oauthlib<0.5,>=0.4.1
Downloading google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Collecting markdown>=2.6.8
Downloading Markdown-3.4.1-py3-none-any.whl (93 kB)
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Collecting cachetools<6.0,>=2.0.0
Downloading cachetools-5.2.0-py3-none-any.whl (9.3 kB)
Collecting rsa<5,>=3.1.4
Downloading rsa-4.9-py3-none-any.whl (34 kB)
Collecting pyasn1-modules>=0.2.1
Downloading pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
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Collecting requests-oauthlib>=0.7.0
Downloading requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB)
Collecting importlib-metadata>=4.4
Downloading importlib_metadata-4.12.0-py3-none-any.whl (21 kB)
Collecting MarkupSafe>=2.1.1
Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting zipp>=0.5
Downloading zipp-3.8.1-py3-none-any.whl (5.6 kB)
Collecting pyasn1<0.5.0,>=0.4.6
Downloading pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
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Collecting oauthlib>=3.0.0
Downloading oauthlib-3.2.0-py3-none-any.whl (151 kB)
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Building wheels for collected packages: jax, termcolor, wrapt
Building wheel for jax (setup.py): started
Building wheel for jax (setup.py): finished with status 'done'
Created wheel for jax: filename=jax-0.2.14-py3-none-any.whl size=771334 sha256=88ce3f87ab3f21afaa48e225619bf146c5ac48d84c26d938fc31f3e0a953d6c2
Stored in directory: /root/.cache/pip/wheels/ec/bd/25/923906d87d262ee0be5c68b248d1a8249d028603582a256266
Building wheel for termcolor (setup.py): started
Building wheel for termcolor (setup.py): finished with status 'done'
Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4832 sha256=29307edcd95d738c0534abb583bc7b5ed030528ebc20993545351080aceede78
Stored in directory: /root/.cache/pip/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
Building wheel for wrapt (setup.py): started
Building wheel for wrapt (setup.py): finished with status 'done'
Created wheel for wrapt: filename=wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl size=70825 sha256=098a53bd28ce41406aa898f38e846cd6b23e598011f238dd6fa886787c675eb9
Stored in directory: /root/.cache/pip/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6
Successfully built jax termcolor wrapt
Installing collected packages: wrapt, typing-extensions, termcolor, tensorflow-estimator, tensorboard-plugin-wit, pytz, pyasn1, keras-nightly, flatbuffers, cached-property, zipp, websocket-client, tensorboard-data-server, tabulate, six, rsa, PyYAML, pyasn1-modules, protobuf, oauthlib, numpy, MarkupSafe, immutabledict, gast, contextlib2, cachetools, werkzeug, scipy, requests-oauthlib, python-dateutil, opt_einsum, keras-preprocessing, importlib-metadata, h5py, grpcio, google-pasta, google-auth, docker, dm-tree, biopython, astunparse, absl-py, pandas, ml-collections, markdown, jaxlib, jax, google-auth-oauthlib, dm-haiku, tensorboard, chex, tensorflow-cpu
Attempting uninstall: six
Found existing installation: six 1.16.0
Uninstalling six-1.16.0:
Successfully uninstalled six-1.16.0
Attempting uninstall: numpy
Found existing installation: numpy 1.21.6
Uninstalling numpy-1.21.6:
Successfully uninstalled numpy-1.21.6
Successfully installed MarkupSafe-2.1.1 PyYAML-6.0 absl-py-0.13.0 astunparse-1.6.3 biopython-1.79 cached-property-1.5.2 cachetools-5.2.0 chex-0.0.7 contextlib2-21.6.0 dm-haiku-0.0.4 dm-tree-0.1.6 docker-5.0.0 flatbuffers-1.12 gast-0.4.0 google-auth-2.10.0 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.34.1 h5py-3.1.0 immutabledict-2.0.0 importlib-metadata-4.12.0 jax-0.2.14 jaxlib-0.3.15 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 markdown-3.4.1 ml-collections-0.1.0 numpy-1.19.5 oauthlib-3.2.0 opt_einsum-3.3.0 pandas-1.3.4 protobuf-3.20.1 pyasn1-0.4.8 pyasn1-modules-0.2.8 python-dateutil-2.8.2 pytz-2022.2.1 requests-oauthlib-1.3.1 rsa-4.9 scipy-1.7.0 six-1.15.0 tabulate-0.8.10 tensorboard-2.9.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tensorflow-cpu-2.5.0 tensorflow-estimator-2.5.0 termcolor-1.1.0 typing-extensions-3.7.4.3 websocket-client-1.3.3 werkzeug-2.2.2 wrapt-1.12.1 zipp-3.8.1
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
Looking in links: https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
Requirement already satisfied: jax==0.2.14 in /opt/conda/lib/python3.7/site-packages (0.2.14)
Collecting jaxlib==0.1.69+cuda111
Downloading https://storage.googleapis.com/jax-releases/cuda111/jaxlib-0.1.69%2Bcuda111-cp37-none-manylinux2010_x86_64.whl (196.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 196.5/196.5 MB 1.5 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.12 in /opt/conda/lib/python3.7/site-packages (from jax==0.2.14) (1.19.5)
Requirement already satisfied: opt-einsum in /opt/conda/lib/python3.7/site-packages (from jax==0.2.14) (3.3.0)
Requirement already satisfied: absl-py in /opt/conda/lib/python3.7/site-packages (from jax==0.2.14) (0.13.0)
Requirement already satisfied: flatbuffers<3.0,>=1.12 in /opt/conda/lib/python3.7/site-packages (from jaxlib==0.1.69+cuda111) (1.12)
Requirement already satisfied: scipy in /opt/conda/lib/python3.7/site-packages (from jaxlib==0.1.69+cuda111) (1.7.0)
Requirement already satisfied: six in /opt/conda/lib/python3.7/site-packages (from absl-py->jax==0.2.14) (1.15.0)
Installing collected packages: jaxlib
Attempting uninstall: jaxlib
Found existing installation: jaxlib 0.3.15
Uninstalling jaxlib-0.3.15:
Successfully uninstalled jaxlib-0.3.15
Successfully installed jaxlib-0.1.69+cuda111
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
Removing intermediate container f99f777d4868
---> c0028331904d
Step 13/18 : WORKDIR /opt/conda/lib/python3.7/site-packages
---> Running in 85498ade152f
Removing intermediate container 85498ade152f
---> 6f3582890aa8
Step 14/18 : RUN patch -p0 < /app/alphafold/docker/openmm.patch
---> Running in b34664dbb490
patching file simtk/openmm/app/topology.py
Hunk #1 succeeded at 353 (offset -3 lines).
Removing intermediate container b34664dbb490
---> b093a8603ba3
Step 15/18 : RUN chmod u+s /sbin/ldconfig.real
---> Running in 27660b373587
Removing intermediate container 27660b373587
---> fea927e976f6
Step 16/18 : WORKDIR /app/alphafold
---> Running in 4cc9547f033a
Removing intermediate container 4cc9547f033a
---> beeccc62dc0d
Step 17/18 : RUN echo $'#!/bin/bash\nldconfig\npython /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh && chmod +x /app/run_alphafold.sh
---> Running in c439edd89a40
Removing intermediate container c439edd89a40
---> 8e4dccb63fd5
Step 18/18 : ENTRYPOINT ["/app/run_alphafold.sh"]
---> Running in 259e07eb252e
Removing intermediate container 259e07eb252e
---> 1db17d1b0e93
Successfully built 1db17d1b0e93
- Install the
run_docker.pydependencies. Note: You may optionally wish to create a Python Virtual Environment to prevent conflicts with your system’s Python environment.
~/alphafold$ pip3 install -r docker/requirements.txt
Command 'pip3' not found, but can be installed with:
sudo apt install python3-pip
Oops.
~/alphafold$ sudo apt install python3-pip
[sudo] password for luolab:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
python-pip-whl python3-setuptools python3-wheel
Suggested packages:
python-setuptools-doc
The following NEW packages will be installed:
python-pip-whl python3-pip python3-setuptools python3-wheel
0 upgraded, 4 newly installed, 0 to remove and 10 not upgraded.
Need to get 2,389 kB of archives.
After this operation, 4,932 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://cn.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-pip-whl all 20.0.2-5ubuntu1.6 [1,805 kB]
Get:2 http://cn.archive.ubuntu.com/ubuntu focal/main amd64 python3-setuptools all 45.2.0-1 [330 kB]
Get:3 http://cn.archive.ubuntu.com/ubuntu focal/universe amd64 python3-wheel all 0.34.2-1 [23.8 kB]
Get:4 http://cn.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python3-pip all 20.0.2-5ubuntu1.6 [231 kB]
Fetched 2,389 kB in 9s (262 kB/s)
Selecting previously unselected package python-pip-whl.
(Reading database ... 310709 files and directories currently installed.)
Preparing to unpack .../python-pip-whl_20.0.2-5ubuntu1.6_all.deb ...
Unpacking python-pip-whl (20.0.2-5ubuntu1.6) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../python3-setuptools_45.2.0-1_all.deb ...
Unpacking python3-setuptools (45.2.0-1) ...
Selecting previously unselected package python3-wheel.
Preparing to unpack .../python3-wheel_0.34.2-1_all.deb ...
Unpacking python3-wheel (0.34.2-1) ...
Selecting previously unselected package python3-pip.
Preparing to unpack .../python3-pip_20.0.2-5ubuntu1.6_all.deb ...
Unpacking python3-pip (20.0.2-5ubuntu1.6) ...
Setting up python3-setuptools (45.2.0-1) ...
Setting up python3-wheel (0.34.2-1) ...
Setting up python-pip-whl (20.0.2-5ubuntu1.6) ...
Setting up python3-pip (20.0.2-5ubuntu1.6) ...
Processing triggers for man-db (2.9.1-1) ...
First time using Python to manage virtual environments.
(base) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ conda deactivate
luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ python3 -m venv alphafold2
The virtual environment was not created successfully because ensurepip is not
available. On Debian/Ubuntu systems, you need to install the python3-venv
package using the following command.
apt install python3.8-venv
You may need to use sudo with that command. After installing the python3-venv
package, recreate your virtual environment.
Failing command: ['/home/luolab/GITHUB_REPO/alphafold/alphafold2/bin/python3', '-Im', 'ensurepip', '--upgrade', '--default-pip']
luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ sudo apt install python3.8-venv
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
python3.8-venv
0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded.
Need to get 5,444 B of archives.
After this operation, 27.6 kB of additional disk space will be used.
Get:1 http://cn.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python3.8-venv amd64 3.8.10-0ubuntu1~20.04.5 [5,444 B]
Fetched 5,444 B in 1s (8,694 B/s)
Selecting previously unselected package python3.8-venv.
(Reading database ... 311073 files and directories currently installed.)
Preparing to unpack .../python3.8-venv_3.8.10-0ubuntu1~20.04.5_amd64.deb ...
Unpacking python3.8-venv (3.8.10-0ubuntu1~20.04.5) ...
Setting up python3.8-venv (3.8.10-0ubuntu1~20.04.5) ...
luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ python3 -m venv ~/.virtualenvs/alphafold2
luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ source ~/.virtualenvs/alphafold2/bin/activate
Confirm that venv is properly setup:
(alphafold2) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ which python
/home/luolab/.virtualenvs/alphafold2/bin/python
To leave the virtualenv, simply do:
(alphafold2) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ deactivate
Now install dependencies:
(alphafold2) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ pip3 install -r docker/requirements.txt
Collecting absl-py==0.13.0
Using cached absl_py-0.13.0-py3-none-any.whl (132 kB)
Collecting docker==5.0.0
Downloading docker-5.0.0-py2.py3-none-any.whl (146 kB)
|████████████████████████████████| 146 kB 1.1 MB/s
Collecting six
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting websocket-client>=0.32.0
Using cached websocket_client-1.3.3-py3-none-any.whl (54 kB)
Collecting requests!=2.18.0,>=2.14.2
Using cached requests-2.28.1-py3-none-any.whl (62 kB)
Collecting charset-normalizer<3,>=2
Using cached charset_normalizer-2.1.0-py3-none-any.whl (39 kB)
Collecting certifi>=2017.4.17
Using cached certifi-2022.6.15-py3-none-any.whl (160 kB)
Collecting idna<4,>=2.5
Using cached idna-3.3-py3-none-any.whl (61 kB)
Collecting urllib3<1.27,>=1.21.1
Using cached urllib3-1.26.11-py2.py3-none-any.whl (139 kB)
Installing collected packages: six, absl-py, websocket-client, charset-normalizer, certifi, idna, urllib3, requests, docker
Successfully installed absl-py-0.13.0 certifi-2022.6.15 charset-normalizer-2.1.0 docker-5.0.0 idna-3.3 requests-2.28.1 six-1.16.0 urllib3-1.26.11 websocket-client-1.3.3
- Make sure that the output directory exists (the default is
/tmp/alphafold) and that you have sufficient permissions to write into it. You can make sure that is the case by manually runningmkdir /tmp/alphafoldandchmod 770 /tmp/alphafold.
(alphafold2) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ mkdir /tmp/alphafold
(alphafold2) luolab@luolab-Z10PE-D16-WS:~/GITHUB_REPO/alphafold$ chmod 770 /tmp/alphafold/
Last modified on 2022-08-19