Htomlinson14
commented
1 year ago Hi thanks for raising! How many times did you try to build? Looks like a connection time-out
Closed methylome closed 1 year ago
Htomlinson14
commented
1 year ago Hi thanks for raising! How many times did you try to build? Looks like a connection time-out
methylome
commented
1 year ago I keep trying to build. My centos server cannot get http://security.ubuntu.com/ubuntu/pool/main/g/gcc-7/cpp-7_7.5.0-3ubuntu1~18.04_amd64.deb because the downloading was stalled after 2.22M was downloaded. The resolution was to download cpp-7 using iMAC and install it.
RUN apt-get update --fix-missing \
&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
gcc-7-base libisl19 libmpc3 libmpfr6
COPY cpp-7_7.5.0-3ubuntu1~18.04_amd64.deb /tmp
RUN dpkg -i /tmp/cpp-7_7.5.0-3ubuntu1~18.04_amd64.debWith the fix, the following error occurred.
Step 15/21 : RUN pip3 install --upgrade pip --no-cache-dir && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir && pip3 install --upgrade --no-cache-dir jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
---> Running in fc0470b024dc
/bin/bash: pip3: command not found
The command '/bin/bash -o pipefail -c pip3 install --upgrade pip --no-cache-dir && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir && pip3 install --upgrade --no-cache-dir jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html' returned a non-zero code: 127RUN ls -l /opt/conda/bin
Step 13/26 : RUN ls -l /opt/conda/bin
---> Running in 31537d56f5ff
total 34536
-rwxrwxr-x 1 root root 101 Mar 7 00:34 2to3-3.8
-rwxrwxr-x 1 root root 184 Mar 7 00:34 activate
-rwxrwxr-x 2 root root 110256 Jul 15 2019 bunzip2
-rwxrwxr-x 2 root root 110256 Jul 15 2019 bzcat
lrwxrwxrwx 1 root root 6 Mar 7 00:24 bzcmp -> bzdiff
-rwxrwxr-x 2 root root 2140 Jul 15 2019 bzdiff
lrwxrwxrwx 1 root root 6 Mar 7 00:24 bzegrep -> bzgrep
lrwxrwxrwx 1 root root 6 Mar 7 00:24 bzfgrep -> bzgrep
-rwxrwxr-x 2 root root 2054 Jul 15 2019 bzgrep
-rwxrwxr-x 2 root root 110256 Jul 15 2019 bzip2
-rwxrwxr-x 2 root root 21064 Jul 15 2019 bzip2recover
lrwxrwxrwx 1 root root 6 Mar 7 00:24 bzless -> bzmore
-rwxrwxr-x 2 root root 1259 Jul 15 2019 bzmore
-rwxrwxr-x 1 root root 7226 Mar 7 00:34 c_rehash
lrwxrwxrwx 1 root root 3 Mar 7 00:24 captoinfo -> tic
-rwxrwxr-x 2 root root 14312 Jan 26 11:54 clear
-rwxrwxr-x 1 root root 511 Mar 7 00:34 conda
-rwxrwxr-x 1 root root 148 Mar 7 00:34 conda-env
-rwxrwxr-x 1 root root 234 Mar 7 00:34 cph
-rwxrwxr-x 1 root root 272 Mar 7 00:34 deactivate
-rwxrwxr-x 1 root root 254 Mar 7 00:34 f2py
-rwxrwxr-x 1 root root 254 Mar 7 00:34 f2py3
-rwxrwxr-x 1 root root 254 Mar 7 00:34 f2py3.8
-rwxrwxr-x 1 root root 2450264 Dec 4 2021 fftw-wisdom
-rwxrwxr-x 1 root root 2282 Dec 4 2021 fftw-wisdom-to-conf
-rwxrwxr-x 1 root root 2500392 Dec 4 2021 fftwf-wisdom
-rwxrwxr-x 1 root root 1102640 Dec 4 2021 fftwl-wisdom
-rwxrwxr-x 1 root root 99 Mar 7 00:34 idle3.8
-rwxrwxr-x 2 root root 63536 Jan 26 11:54 infocmp
lrwxrwxrwx 1 root root 3 Mar 7 00:24 infotocap -> tic
lrwxrwxrwx 1 root root 2 Mar 7 00:24 lzcat -> xz
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzcmp -> xzdiff
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzdiff -> xzdiff
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzegrep -> xzgrep
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzfgrep -> xzgrep
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzgrep -> xzgrep
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzless -> xzless
lrwxrwxrwx 1 root root 2 Mar 7 00:24 lzma -> xz
-rwxrwxr-x 2 root root 17184 Jan 18 19:39 lzmadec
-rwxrwxr-x 1 root root 17016 Mar 7 00:24 lzmainfo
lrwxrwxrwx 1 root root 6 Mar 7 00:24 lzmore -> xzmore
-rwxrwxr-x 1 root root 8866 Mar 7 00:24 ncursesw6-config
-rwxrwxr-x 1 root root 1094680 May 3 2022 openssl
-rwxr-xr-x 1 root root 227 Mar 7 00:34 pdbfixer
-rwxrwxr-x 1 root root 84 Mar 7 00:34 pydoc3.8
-rwxrwxr-x 1 root root 22751104 Mar 7 00:34 python3.8
-rwxrwxr-x 1 root root 3489 Mar 7 00:34 python3.8-config
lrwxrwxrwx 1 root root 4 Mar 7 00:24 reset -> tset
-rwxrwxr-x 2 root root 1678440 Jan 9 19:53 sqlite3
-rwxrwxr-x 2 root root 30392 Jun 1 2022 sqlite3_analyzer
-rwxrwxr-x 2 root root 22424 Jan 26 11:54 tabs
lrwxrwxrwx 1 root root 8 Mar 7 00:24 tclsh -> tclsh8.6
-rwxrwxr-x 2 root root 16816 Jun 1 2022 tclsh8.6
-rwxrwxr-x 2 root root 92248 Jan 26 11:54 tic
-rwxrwxr-x 2 root root 22424 Jan 26 11:54 toe
-rwxrwxr-x 2 root root 22528 Jan 26 11:54 tput
-rwxrwxr-x 2 root root 30696 Jan 26 11:54 tset
lrwxrwxrwx 1 root root 2 Mar 7 00:24 unlzma -> xz
lrwxrwxrwx 1 root root 2 Mar 7 00:24 unxz -> xz
lrwxrwxrwx 1 root root 7 Mar 7 00:24 wish -> wish8.6
-rwxrwxr-x 2 root root 16968 Jun 1 2022 wish8.6
-rwxrwxr-x 2 root root 2777592 May 19 2022 x86_64-conda-linux-gnu-ld
lrwxrwxrwx 1 root root 25 Mar 7 00:24 x86_64-conda_cos7-linux-gnu-ld -> x86_64-conda-linux-gnu-ld
-rwxrwxr-x 1 root root 95096 Mar 7 00:24 xz
lrwxrwxrwx 1 root root 2 Mar 7 00:24 xzcat -> xz
lrwxrwxrwx 1 root root 6 Mar 7 00:24 xzcmp -> xzdiff
-rwxrwxr-x 2 root root 17184 Jan 18 19:39 xzdec
-rwxrwxr-x 2 root root 7373 Jan 18 19:39 xzdiff
lrwxrwxrwx 1 root root 6 Mar 7 00:24 xzegrep -> xzgrep
lrwxrwxrwx 1 root root 6 Mar 7 00:24 xzfgrep -> xzgrep
-rwxrwxr-x 2 root root 10334 Jan 18 19:39 xzgrep
-rwxrwxr-x 2 root root 1814 Jan 18 19:39 xzless
-rwxrwxr-x 2 root root 2191 Jan 18 19:39 xzmoreThere were no pip3. However
Step 15/26 : RUN python -m pip --version
---> Running in 1309e10b6062
pip 23.0.1 from /opt/conda/lib/python3.8/site-packages/pip (python 3.8)
Step 16/26 : RUN conda list pip
---> Running in 43297f4e4cec
# packages in environment at /opt/conda:
#
# Name Version Build Channel
pip 23.0.1 pyhd8ed1ab_0 conda-forgeSolved by repliacing pip3 with python -m pip.
methylome
commented
1 year ago Another problem was solved by replacing /app/alphafold/docker/openmm.patch with /app/alphafold/openmm.patch
Step 18/22 : RUN patch -p0 < /app/alphafold/docker/openmm.patch
---> Running in 24a6639eab51
/bin/bash: /app/alphafold/docker/openmm.patch: No such file or directory
I tried to build an image for alphafold, but failed with errors below.