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Docker building error due to python requirements #32

Open
bschilder opened this issue Jun 22, 2022 · 1 comment
Open

Docker building error due to python requirements #32

bschilder opened this issue Jun 22, 2022 · 1 comment

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@bschilder
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bschilder commented Jun 22, 2022 •
edited
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Hi @kausmees, I seem to be having some issues setting up the Docker container, which I think stems from installing the python requirements.

Reprex

git clone https://github.com/kausmees/GenoCAE.git
cd GenoCAE
docker build -t gcae/genocae:build -f docker/build.dockerfile .

Output

Here is the full output, but the main error comes at the very end.

Sending build context to Docker daemon  5.337MB
Step 1/14 : ARG CUDA_VERSION=11.1.1
Step 2/14 : ARG OS_VERSION=20.04
Step 3/14 : FROM nvidia/cuda:${CUDA_VERSION}-cudnn8-devel-ubuntu${OS_VERSION}
 ---> 75f53d2b5da8
Step 4/14 : LABEL maintainer="Dong Wang"
 ---> Using cache
 ---> 05c68a023e26
Step 5/14 : ENV PATH="/root/miniconda3/bin:${PATH}"
 ---> Using cache
 ---> 84aafea13cc7
Step 6/14 : ARG PATH="/root/miniconda3/bin:${PATH}"
 ---> Using cache
 ---> d5d84110b3c8
Step 7/14 : ARG DEBIAN_FRONTEND=noninteractive
 ---> Running in 79a5ae18bf31
Removing intermediate container 79a5ae18bf31
 ---> a9ec0c06e8ee
Step 8/14 : SHELL ["/bin/bash", "-c"]
 ---> Running in 07a8435b31cd
Removing intermediate container 07a8435b31cd
 ---> bb8387371d5a
Step 9/14 : RUN apt-get update && apt-get upgrade -y &&apt-get install -y wget python3-pip
 ---> Running in 07b6d6f53352
Get:1 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
Get:2 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]
Get:3 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]
Get:4 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  InRelease [1581 B]
Get:5 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1275 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
Get:9 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]
Get:10 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [30.3 kB]
Get:11 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1161 kB]
Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [2415 kB]
Get:13 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [1404 kB]
Get:14 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [27.1 kB]
Get:15 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [54.2 kB]
Get:16 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  Packages [579 kB]
Get:17 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [27.5 kB]
Get:18 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [1324 kB]
Get:19 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [881 kB]
Get:20 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [1974 kB]
Fetched 23.3 MB in 2s (13.5 MB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages have been kept back:
  libcudnn8 libcudnn8-dev libnccl-dev libnccl2
The following packages will be upgraded:
  apt ca-certificates dpkg dpkg-dev e2fsprogs libapt-pkg6.0 libc-bin
  libcom-err2 libdpkg-perl libext2fs2 libpcre3 libsepol1 libss2 libssl1.1
  libsystemd0 libudev1 linux-libc-dev login logsave openssl passwd
21 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Need to get 10.6 MB of archives.
After this operation, 22.5 kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 dpkg amd64 1.19.7ubuntu3.2 [1128 kB]
Get:2 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 login amd64 1:4.8.1-1ubuntu5.20.04.2 [220 kB]
Get:3 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libc-bin amd64 2.31-0ubuntu9.9 [633 kB]
Get:4 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsystemd0 amd64 245.4-4ubuntu3.17 [269 kB]
Get:5 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libudev1 amd64 245.4-4ubuntu3.17 [76.5 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libapt-pkg6.0 amd64 2.0.9 [839 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 apt amd64 2.0.9 [1294 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 logsave amd64 1.45.5-2ubuntu1.1 [10.2 kB]
Get:9 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libext2fs2 amd64 1.45.5-2ubuntu1.1 [183 kB]
Get:10 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 e2fsprogs amd64 1.45.5-2ubuntu1.1 [527 kB]
Get:11 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpcre3 amd64 2:8.39-12ubuntu0.1 [232 kB]
Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsepol1 amd64 3.0-1ubuntu0.1 [252 kB]
Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 passwd amd64 1:4.8.1-1ubuntu5.20.04.2 [797 kB]
Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcom-err2 amd64 1.45.5-2ubuntu1.1 [9548 B]
Get:15 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libss2 amd64 1.45.5-2ubuntu1.1 [11.3 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu2.15 [1321 kB]
Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 openssl amd64 1.1.1f-1ubuntu2.15 [623 kB]
Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 ca-certificates all 20211016~20.04.1 [144 kB]
Get:19 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 dpkg-dev all 1.19.7ubuntu3.2 [679 kB]
Get:20 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libdpkg-perl all 1.19.7ubuntu3.2 [231 kB]
Get:21 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 linux-libc-dev amd64 5.4.0-120.136 [1113 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 10.6 MB in 0s (55.0 MB/s)
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../dpkg_1.19.7ubuntu3.2_amd64.deb ...
Unpacking dpkg (1.19.7ubuntu3.2) over (1.19.7ubuntu3) ...
Setting up dpkg (1.19.7ubuntu3.2) ...
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../login_1%3a4.8.1-1ubuntu5.20.04.2_amd64.deb ...
Unpacking login (1:4.8.1-1ubuntu5.20.04.2) over (1:4.8.1-1ubuntu5.20.04.1) ...
Setting up login (1:4.8.1-1ubuntu5.20.04.2) ...
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../libc-bin_2.31-0ubuntu9.9_amd64.deb ...
Unpacking libc-bin (2.31-0ubuntu9.9) over (2.31-0ubuntu9.7) ...
Setting up libc-bin (2.31-0ubuntu9.9) ...
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../libsystemd0_245.4-4ubuntu3.17_amd64.deb ...
Unpacking libsystemd0:amd64 (245.4-4ubuntu3.17) over (245.4-4ubuntu3.16) ...
Setting up libsystemd0:amd64 (245.4-4ubuntu3.17) ...
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../libudev1_245.4-4ubuntu3.17_amd64.deb ...
Unpacking libudev1:amd64 (245.4-4ubuntu3.17) over (245.4-4ubuntu3.16) ...
Setting up libudev1:amd64 (245.4-4ubuntu3.17) ...
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../libapt-pkg6.0_2.0.9_amd64.deb ...
Unpacking libapt-pkg6.0:amd64 (2.0.9) over (2.0.6) ...
Setting up libapt-pkg6.0:amd64 (2.0.9) ...
(Reading database ... 12626 files and directories currently installed.)
Preparing to unpack .../archives/apt_2.0.9_amd64.deb ...
Unpacking apt (2.0.9) over (2.0.6) ...
Setting up apt (2.0.9) ...
Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ...
(Reading database ... 12625 files and directories currently installed.)
Preparing to unpack .../logsave_1.45.5-2ubuntu1.1_amd64.deb ...
Unpacking logsave (1.45.5-2ubuntu1.1) over (1.45.5-2ubuntu1) ...
Preparing to unpack .../libext2fs2_1.45.5-2ubuntu1.1_amd64.deb ...
Unpacking libext2fs2:amd64 (1.45.5-2ubuntu1.1) over (1.45.5-2ubuntu1) ...
Setting up libext2fs2:amd64 (1.45.5-2ubuntu1.1) ...
(Reading database ... 12625 files and directories currently installed.)
Preparing to unpack .../e2fsprogs_1.45.5-2ubuntu1.1_amd64.deb ...
Unpacking e2fsprogs (1.45.5-2ubuntu1.1) over (1.45.5-2ubuntu1) ...
Preparing to unpack .../libpcre3_2%3a8.39-12ubuntu0.1_amd64.deb ...
Unpacking libpcre3:amd64 (2:8.39-12ubuntu0.1) over (2:8.39-12build1) ...
Setting up libpcre3:amd64 (2:8.39-12ubuntu0.1) ...
(Reading database ... 12625 files and directories currently installed.)
Preparing to unpack .../libsepol1_3.0-1ubuntu0.1_amd64.deb ...
Unpacking libsepol1:amd64 (3.0-1ubuntu0.1) over (3.0-1) ...
Setting up libsepol1:amd64 (3.0-1ubuntu0.1) ...
(Reading database ... 12625 files and directories currently installed.)
Preparing to unpack .../passwd_1%3a4.8.1-1ubuntu5.20.04.2_amd64.deb ...
Unpacking passwd (1:4.8.1-1ubuntu5.20.04.2) over (1:4.8.1-1ubuntu5.20.04.1) ...
Setting up passwd (1:4.8.1-1ubuntu5.20.04.2) ...
(Reading database ... 12625 files and directories currently installed.)
Preparing to unpack .../0-libcom-err2_1.45.5-2ubuntu1.1_amd64.deb ...
Unpacking libcom-err2:amd64 (1.45.5-2ubuntu1.1) over (1.45.5-2ubuntu1) ...
Preparing to unpack .../1-libss2_1.45.5-2ubuntu1.1_amd64.deb ...
Unpacking libss2:amd64 (1.45.5-2ubuntu1.1) over (1.45.5-2ubuntu1) ...
Preparing to unpack .../2-libssl1.1_1.1.1f-1ubuntu2.15_amd64.deb ...
Unpacking libssl1.1:amd64 (1.1.1f-1ubuntu2.15) over (1.1.1f-1ubuntu2.13) ...
Preparing to unpack .../3-openssl_1.1.1f-1ubuntu2.15_amd64.deb ...
Unpacking openssl (1.1.1f-1ubuntu2.15) over (1.1.1f-1ubuntu2.13) ...
Preparing to unpack .../4-ca-certificates_20211016~20.04.1_all.deb ...
Unpacking ca-certificates (20211016~20.04.1) over (20210119~20.04.2) ...
Preparing to unpack .../5-dpkg-dev_1.19.7ubuntu3.2_all.deb ...
Unpacking dpkg-dev (1.19.7ubuntu3.2) over (1.19.7ubuntu3) ...
Preparing to unpack .../6-libdpkg-perl_1.19.7ubuntu3.2_all.deb ...
Unpacking libdpkg-perl (1.19.7ubuntu3.2) over (1.19.7ubuntu3) ...
Preparing to unpack .../7-linux-libc-dev_5.4.0-120.136_amd64.deb ...
Unpacking linux-libc-dev:amd64 (5.4.0-120.136) over (5.4.0-113.127) ...
Setting up libssl1.1:amd64 (1.1.1f-1ubuntu2.15) ...
Setting up linux-libc-dev:amd64 (5.4.0-120.136) ...
Setting up libcom-err2:amd64 (1.45.5-2ubuntu1.1) ...
Setting up libss2:amd64 (1.45.5-2ubuntu1.1) ...
Setting up libdpkg-perl (1.19.7ubuntu3.2) ...
Setting up logsave (1.45.5-2ubuntu1.1) ...
Setting up openssl (1.1.1f-1ubuntu2.15) ...
Setting up e2fsprogs (1.45.5-2ubuntu1.1) ...
Setting up dpkg-dev (1.19.7ubuntu3.2) ...
Setting up ca-certificates (20211016~20.04.1) ...
Updating certificates in /etc/ssl/certs...
rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL
7 added, 8 removed; done.
Processing triggers for libc-bin (2.31-0ubuntu9.9) ...
Processing triggers for ca-certificates (20211016~20.04.1) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  file libexpat1 libexpat1-dev libmagic-mgc libmagic1 libmpdec2 libpsl5
  libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev
  libpython3.8-minimal libpython3.8-stdlib mime-support publicsuffix
  python-pip-whl python3 python3-dev python3-distutils python3-lib2to3
  python3-minimal python3-pkg-resources python3-setuptools python3-wheel
  python3.8 python3.8-dev python3.8-minimal zlib1g-dev
Suggested packages:
  python3-doc python3-tk python3-venv python-setuptools-doc python3.8-venv
  python3.8-doc binfmt-support
The following NEW packages will be installed:
  file libexpat1 libexpat1-dev libmagic-mgc libmagic1 libmpdec2 libpsl5
  libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev
  libpython3.8-minimal libpython3.8-stdlib mime-support publicsuffix
  python-pip-whl python3 python3-dev python3-distutils python3-lib2to3
  python3-minimal python3-pip python3-pkg-resources python3-setuptools
  python3-wheel python3.8 python3.8-dev python3.8-minimal wget zlib1g-dev
0 upgraded, 30 newly installed, 0 to remove and 4 not upgraded.
Need to get 14.9 MB of archives.
After this operation, 63.1 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-minimal amd64 3.8.10-0ubuntu1~20.04.4 [717 kB]
Get:2 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libexpat1 amd64 2.2.9-1ubuntu0.4 [74.4 kB]
Get:3 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3.8-minimal amd64 3.8.10-0ubuntu1~20.04.4 [1899 kB]
Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-minimal amd64 3.8.2-0ubuntu2 [23.6 kB]
Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-stdlib amd64 3.8.10-0ubuntu1~20.04.4 [1675 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3.8 amd64 3.8.10-0ubuntu1~20.04.4 [387 kB]
Get:9 http://archive.ubuntu.com/ubuntu focal/main amd64 libpython3-stdlib amd64 3.8.2-0ubuntu2 [7068 B]
Get:10 http://archive.ubuntu.com/ubuntu focal/main amd64 python3 amd64 3.8.2-0ubuntu2 [47.6 kB]
Get:11 http://archive.ubuntu.com/ubuntu focal/main amd64 libmagic-mgc amd64 1:5.38-4 [218 kB]
Get:12 http://archive.ubuntu.com/ubuntu focal/main amd64 libmagic1 amd64 1:5.38-4 [75.9 kB]
Get:13 http://archive.ubuntu.com/ubuntu focal/main amd64 file amd64 1:5.38-4 [23.3 kB]
Get:14 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-pkg-resources all 45.2.0-1 [130 kB]
Get:15 http://archive.ubuntu.com/ubuntu focal/main amd64 libpsl5 amd64 0.21.0-1ubuntu1 [51.5 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal/main amd64 publicsuffix all 20200303.0012-1 [111 kB]
Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 wget amd64 1.20.3-1ubuntu2 [348 kB]
Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libexpat1-dev amd64 2.2.9-1ubuntu0.4 [117 kB]
Get:19 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8 amd64 3.8.10-0ubuntu1~20.04.4 [1625 kB]
Get:20 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-dev amd64 3.8.10-0ubuntu1~20.04.4 [3952 kB]
Get:21 http://archive.ubuntu.com/ubuntu focal/main amd64 libpython3-dev amd64 3.8.2-0ubuntu2 [7236 B]
Get:22 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-pip-whl all 20.0.2-5ubuntu1.6 [1805 kB]
Get:23 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu1.3 [155 kB]
Get:24 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3.8-dev amd64 3.8.10-0ubuntu1~20.04.4 [514 kB]
Get:25 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-lib2to3 all 3.8.10-0ubuntu1~20.04 [76.3 kB]
Get:26 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-distutils all 3.8.10-0ubuntu1~20.04 [141 kB]
Get:27 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-dev amd64 3.8.2-0ubuntu2 [1212 B]
Get:28 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-setuptools all 45.2.0-1 [330 kB]
Get:29 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-wheel all 0.34.2-1 [23.8 kB]
Get:30 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 python3-pip all 20.0.2-5ubuntu1.6 [231 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 14.9 MB in 0s (81.4 MB/s)
Selecting previously unselected package libpython3.8-minimal:amd64.
(Reading database ... 12624 files and directories currently installed.)
Preparing to unpack .../libpython3.8-minimal_3.8.10-0ubuntu1~20.04.4_amd64.deb ...
Unpacking libpython3.8-minimal:amd64 (3.8.10-0ubuntu1~20.04.4) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.2.9-1ubuntu0.4_amd64.deb ...
Unpacking libexpat1:amd64 (2.2.9-1ubuntu0.4) ...
Selecting previously unselected package python3.8-minimal.
Preparing to unpack .../python3.8-minimal_3.8.10-0ubuntu1~20.04.4_amd64.deb ...
Unpacking python3.8-minimal (3.8.10-0ubuntu1~20.04.4) ...
Setting up libpython3.8-minimal:amd64 (3.8.10-0ubuntu1~20.04.4) ...
Setting up libexpat1:amd64 (2.2.9-1ubuntu0.4) ...
Setting up python3.8-minimal (3.8.10-0ubuntu1~20.04.4) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 12915 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_amd64.deb ...
Unpacking python3-minimal (3.8.2-0ubuntu2) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../1-mime-support_3.64ubuntu1_all.deb ...
Unpacking mime-support (3.64ubuntu1) ...
Selecting previously unselected package libmpdec2:amd64.
Preparing to unpack .../2-libmpdec2_2.4.2-3_amd64.deb ...
Unpacking libmpdec2:amd64 (2.4.2-3) ...
Selecting previously unselected package libpython3.8-stdlib:amd64.
Preparing to unpack .../3-libpython3.8-stdlib_3.8.10-0ubuntu1~20.04.4_amd64.deb ...
Unpacking libpython3.8-stdlib:amd64 (3.8.10-0ubuntu1~20.04.4) ...
Selecting previously unselected package python3.8.
Preparing to unpack .../4-python3.8_3.8.10-0ubuntu1~20.04.4_amd64.deb ...
Unpacking python3.8 (3.8.10-0ubuntu1~20.04.4) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../5-libpython3-stdlib_3.8.2-0ubuntu2_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.8.2-0ubuntu2) ...
Setting up python3-minimal (3.8.2-0ubuntu2) ...
Selecting previously unselected package python3.
(Reading database ... 13317 files and directories currently installed.)
Preparing to unpack .../00-python3_3.8.2-0ubuntu2_amd64.deb ...
Unpacking python3 (3.8.2-0ubuntu2) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.38-4_amd64.deb ...
Unpacking libmagic-mgc (1:5.38-4) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../02-libmagic1_1%3a5.38-4_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.38-4) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.38-4_amd64.deb ...
Unpacking file (1:5.38-4) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../04-python3-pkg-resources_45.2.0-1_all.deb ...
Unpacking python3-pkg-resources (45.2.0-1) ...
Selecting previously unselected package libpsl5:amd64.
Preparing to unpack .../05-libpsl5_0.21.0-1ubuntu1_amd64.deb ...
Unpacking libpsl5:amd64 (0.21.0-1ubuntu1) ...
Selecting previously unselected package publicsuffix.
Preparing to unpack .../06-publicsuffix_20200303.0012-1_all.deb ...
Unpacking publicsuffix (20200303.0012-1) ...
Selecting previously unselected package wget.
Preparing to unpack .../07-wget_1.20.3-1ubuntu2_amd64.deb ...
Unpacking wget (1.20.3-1ubuntu2) ...
Selecting previously unselected package libexpat1-dev:amd64.
Preparing to unpack .../08-libexpat1-dev_2.2.9-1ubuntu0.4_amd64.deb ...
Unpacking libexpat1-dev:amd64 (2.2.9-1ubuntu0.4) ...
Selecting previously unselected package libpython3.8:amd64.
Preparing to unpack .../09-libpython3.8_3.8.10-0ubuntu1~20.04.4_amd64.deb ...
Unpacking libpython3.8:amd64 (3.8.10-0ubuntu1~20.04.4) ...
Selecting previously unselected package libpython3.8-dev:amd64.
Preparing to unpack .../10-libpython3.8-dev_3.8.10-0ubuntu1~20.04.4_amd64.deb ...
Unpacking libpython3.8-dev:amd64 (3.8.10-0ubuntu1~20.04.4) ...
Selecting previously unselected package libpython3-dev:amd64.
Preparing to unpack .../11-libpython3-dev_3.8.2-0ubuntu2_amd64.deb ...
Unpacking libpython3-dev:amd64 (3.8.2-0ubuntu2) ...
Selecting previously unselected package python-pip-whl.
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Step 10/14 : RUN python3 -m pip install --no-cache-dir --upgrade pip
 ---> Running in a7851101a995
Collecting pip
  Downloading pip-22.1.2-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 20.0.2
    Not uninstalling pip at /usr/lib/python3/dist-packages, outside environment /usr
    Can't uninstall 'pip'. No files were found to uninstall.
Successfully installed pip-22.1.2
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Step 11/14 : WORKDIR /workspace
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Step 12/14 : ADD ./requirements.txt /workspace
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Step 13/14 : RUN python3 -m pip install -r /workspace/requirements.txt and &&rm /workspace/requirements.txt
 ---> Running in df9be31afa55
ERROR: Could not find a version that satisfies the requirement and (from versions: none)
ERROR: No matching distribution found for and
The command '/bin/bash -c python3 -m pip install -r /workspace/requirements.txt and &&rm /workspace/requirements.txt' returned a non-zero code: 1

Potential solutions

One way to avoid this might be to make use of conda environments with less restrictive version requirements. I've created a yaml file which can be used to set up all the dependencies. Haven't yet tried running GenoCAE with it yet though.
Perhaps this could be used when setting up the Docker container, instead of the requirements.txt file? (PS- only added the .txt suffix to allow it to be uploaded to GH Issues).

Thanks! Really looking forward to using GenoCAE!
env.yml.txt

conda env create -f env.yml.txt

Best,
Brian
@bschilder
Copy link
Author

I can confirm that using the conda env (without the Docker, on Linux) seems to work for the example training!

python3 run_gcae.py train --datadir example_tiny/ --data HumanOrigins249_tiny --model_id M1  --epochs 20 --save_interval 2  --train_opts_id ex3  --data_opts_id b_0_4

Output

tensorflow version 2.8.1

______________________________ arguments ______________________________
train : True
datadir : example_tiny/
data : HumanOrigins249_tiny
model_id : M1
train_opts_id : ex3
data_opts_id : b_0_4
epochs : 20
resume_from : None
trainedmodeldir : None
patience : None
save_interval : 2
start_saving_from : None
project : False
superpops : None
epoch : None
pdata : None
trainedmodelname : None
plot : False
animate : False
evaluate : False
metrics : None

______________________________ data opts ______________________________
sparsifies : [0.0, 0.1, 0.2, 0.3, 0.4]
norm_opts : {'flip': False, 'missing_val': -1.0}
norm_mode : genotypewise01
impute_missing : True
validation_split : 0.2

______________________________ train opts ______________________________
learning_rate : 0.00032
batch_size : 10
noise_std : 0.0032
n_samples : -1
loss : {'module': 'tf.keras.losses', 'class': 'CategoricalCrossentropy', 'args': {'from_logits': False}}
regularizer : {'reg_factor': 1e-07, 'module': 'tf.keras.regularizers', 'class': 'l2'}
lr_scheme : {'module': 'tf.keras.optimizers.schedules', 'class': 'ExponentialDecay', 'args': {'decay_rate': 0.96, 'decay_steps': 100, 'staircase': False}}
______________________________
Imputing originally missing genotypes to most common value.
Reading ind pop list from /shared/bms20/projects/GenoCAE/example_tiny//HumanOrigins249_tiny.fam
Reading ind pop list from /shared/bms20/projects/GenoCAE/example_tiny//HumanOrigins249_tiny.fam
2022-06-22 14:41:35.362082: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Using learning rate schedule tf.keras.optimizers.schedules.ExponentialDecay with {'decay_rate': 0.96, 'decay_steps': 100, 'staircase': False}

______________________________ Data ______________________________
N unique train samples: 199
--- training on : 199
N valid samples: 50
N markers: 9259


______________________________ Building model ______________________________
Adding layer: Conv1D: {'filters': 8, 'kernel_size': 5, 'padding': 'same', 'strides': 1}
Adding layer: BatchNormalization: {}
Adding layer: ResidualBlock2: {'filters': 8, 'kernel_size': 5}
--- conv1d  filters: 8 kernel_size: 5
--- batch normalization
--- conv1d  filters: 8 kernel_size: 5
--- batch normalization
Adding layer: MaxPooling1D: {'pool_size': 5, 'strides': 2, 'padding': 'same'}
Adding layer: Conv1D: {'filters': 8, 'kernel_size': 5, 'padding': 'same', 'activation': 'elu'}
Adding layer: BatchNormalization: {}
Adding layer: Flatten: {}
Adding layer: Dropout: {'rate': 0.01}
Adding layer: Dense: {'units': 75}
Adding layer: Dropout: {'rate': 0.01}
Adding layer: Dense: {'units': 75, 'activation': 'elu'}
Adding layer: Dense: {'units': 2, 'name': 'encoded'}
Adding layer: Dense: {'units': 75, 'activation': 'elu'}
Adding layer: Dropout: {'rate': 0.01}
Adding layer: Dense: {'units': 75, 'activation': 'elu'}
Adding layer: Dropout: {'rate': 0.01}
Adding layer: Dense: {'units': 37040}
Adding layer: Reshape: {'target_shape': (4630, 8), 'name': 'i_msvar'}
Adding layer: Conv1D: {'filters': 8, 'kernel_size': 5, 'padding': 'same', 'activation': 'elu'}
Adding layer: BatchNormalization: {}
Adding layer: Reshape: {'target_shape': (4630, 1, 8)}
Adding layer: UpSampling2D: {'size': (2, 1)}
Adding layer: Reshape: {'target_shape': (9260, 8)}
Adding layer: ResidualBlock2: {'filters': 8, 'kernel_size': 5}
--- conv1d  filters: 8 kernel_size: 5
--- batch normalization
--- conv1d  filters: 8 kernel_size: 5
--- batch normalization
Adding layer: Conv1D: {'filters': 8, 'kernel_size': 5, 'padding': 'same', 'activation': 'elu', 'name': 'nms'}
Adding layer: BatchNormalization: {}
Adding layer: Conv1D: {'filters': 1, 'kernel_size': 1, 'padding': 'same'}
Adding layer: Flatten: {'name': 'logits'}

______________________________ Train ______________________________
Model layers and dimensions:
-----------------------------
In DG.get_train_set: number of -1.0 genotypes in train: 0
In DG.get_train_set: number of -9 genotypes in train: 0
In DG.get_train_set: number of 0 values in train mask: 0
inputs shape (2, 9259, 3)
layer 1
--- type: <class 'keras.layers.convolutional.Conv1D'>
--- shape: (2, 9259, 8)
layer 2: batch_normalization (<class 'keras.layers.normalization.batch_normalization.BatchNormalization'>) 
--- shape: (2, 9259, 8)
layer 3: res_block1 (<class 'utils.layers.ResidualBlock2'>) 
--- shape: (2, 9259, 8)
layer 4: max_pooling1d (<class 'keras.layers.pooling.MaxPooling1D'>) 
--- shape: (2, 4630, 8)
layer 5: conv1d_3 (<class 'keras.layers.convolutional.Conv1D'>) 
--- shape: (2, 4630, 8)
layer 6: batch_normalization_3 (<class 'keras.layers.normalization.batch_normalization.BatchNormalization'>) 
--- shape: (2, 4630, 8)
layer 7: flatten (<class 'keras.layers.core.flatten.Flatten'>) 
--- shape: (2, 37040)
layer 8: dropout (<class 'keras.layers.core.dropout.Dropout'>) 
--- shape: (2, 37040)
layer 9: dense (<class 'keras.layers.core.dense.Dense'>) 
--- shape: (2, 75)
layer 10: dropout_1 (<class 'keras.layers.core.dropout.Dropout'>) 
--- shape: (2, 75)
layer 11: dense_1 (<class 'keras.layers.core.dense.Dense'>) 
--- shape: (2, 75)
layer 12: encoded (<class 'keras.layers.core.dense.Dense'>) 
--- shape: (2, 2)
layer 13: dense_2 (<class 'keras.layers.core.dense.Dense'>) 
--- shape: (2, 75)
layer 14: dropout_2 (<class 'keras.layers.core.dropout.Dropout'>) 
--- shape: (2, 75)
layer 15: dense_3 (<class 'keras.layers.core.dense.Dense'>) 
--- shape: (2, 75)
layer 16: dropout_3 (<class 'keras.layers.core.dropout.Dropout'>) 
--- shape: (2, 75)
layer 17: dense_4 (<class 'keras.layers.core.dense.Dense'>) 
--- shape: (2, 37040)
layer 18: i_msvar (<class 'keras.layers.core.reshape.Reshape'>) 
----- injecting marker-specific variable
ms var (1, 9259)
ms tiled (2, 4630, 2)
concatting: (2, 4630, 8) (2, 4630, 2)
--- shape: (2, 4630, 10)
layer 19: conv1d_4 (<class 'keras.layers.convolutional.Conv1D'>) 
--- shape: (2, 4630, 8)
layer 20: batch_normalization_4 (<class 'keras.layers.normalization.batch_normalization.BatchNormalization'>) 
--- shape: (2, 4630, 8)
layer 21: reshape (<class 'keras.layers.core.reshape.Reshape'>) 
--- shape: (2, 4630, 1, 8)
layer 22: up_sampling2d (<class 'keras.layers.convolutional.UpSampling2D'>) 
--- shape: (2, 9260, 1, 8)
layer 23: reshape_1 (<class 'keras.layers.core.reshape.Reshape'>) 
--- shape: (2, 9260, 8)
layer 24: res_block1 (<class 'utils.layers.ResidualBlock2'>) 
--- shape: (2, 9260, 8)
layer 25: nms (<class 'keras.layers.convolutional.Conv1D'>) 
----- injecting marker-specific variable
ms var (1, 9259)
ms tiled (2, 9260, 1)
concatting: (2, 9260, 8) (2, 9260, 1)
--- shape: (2, 9260, 9)
layer 26: batch_normalization_7 (<class 'keras.layers.normalization.batch_normalization.BatchNormalization'>) 
--- shape: (2, 9260, 9)
layer 27: conv1d_7 (<class 'keras.layers.convolutional.Conv1D'>) 
--- shape: (2, 9260, 1)
layer 28: logits (<class 'keras.layers.core.flatten.Flatten'>) 
--- shape: (2, 9260)

Epoch: 1/20...
--- Train loss: 1.0224  time: 5.308197
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.1 time: 0.678862
--- Valid loss: 0.7322  time: 1.218225 min loss: 0.7322 epochs since: 0

Epoch: 2/20...
--- Train loss: 0.6687  time: 1.154477
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.2 time: 0.635743
--- Valid loss: 0.6321  time: 1.198419 min loss: 0.6321 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/2 time: 0.543809

Epoch: 3/20...
--- Train loss: 0.6181  time: 1.244303
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.3 time: 0.419289
--- Valid loss: 0.6050  time: 0.20956 min loss: 0.6050 epochs since: 0

Epoch: 4/20...
--- Train loss: 0.5983  time: 1.061819
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.4 time: 0.371748
--- Valid loss: 0.5920  time: 0.214656 min loss: 0.5920 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/4 time: 0.37357

Epoch: 5/20...
--- Train loss: 0.5879  time: 1.111482
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.5 time: 0.373572
--- Valid loss: 0.5835  time: 0.28276 min loss: 0.5835 epochs since: 0

Epoch: 6/20...
--- Train loss: 0.5815  time: 1.095755
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.6 time: 0.657343
--- Valid loss: 0.5785  time: 0.203649 min loss: 0.5785 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/6 time: 0.571827

Epoch: 7/20...
--- Train loss: 0.5771  time: 1.05242
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.7 time: 0.559362
--- Valid loss: 0.5750  time: 0.231682 min loss: 0.5750 epochs since: 0

Epoch: 8/20...
--- Train loss: 0.5743  time: 1.03746
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.8 time: 0.541524
--- Valid loss: 0.5723  time: 0.219447 min loss: 0.5723 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/8 time: 0.519319

Epoch: 9/20...
--- Train loss: 0.5713  time: 1.147856
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.9 time: 0.569149
--- Valid loss: 0.5690  time: 0.258631 min loss: 0.5690 epochs since: 0

Epoch: 10/20...
--- Train loss: 0.5700  time: 1.108313
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.10 time: 0.53631
--- Valid loss: 0.5665  time: 0.28765 min loss: 0.5665 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/10 time: 0.463701

Epoch: 11/20...
--- Train loss: 0.5662  time: 1.066851
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.11 time: 0.404494
--- Valid loss: 0.5619  time: 0.206972 min loss: 0.5619 epochs since: 0

Epoch: 12/20...
--- Train loss: 0.5613  time: 1.060015
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.12 time: 0.408927
--- Valid loss: 0.5571  time: 0.214158 min loss: 0.5571 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/12 time: 0.555582

Epoch: 13/20...
--- Train loss: 0.5598  time: 1.061446
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.13 time: 0.400727
--- Valid loss: 0.5531  time: 0.22324 min loss: 0.5531 epochs since: 0

Epoch: 14/20...
--- Train loss: 0.5539  time: 1.096088
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.14 time: 0.39209
--- Valid loss: 0.5500  time: 0.213424 min loss: 0.5500 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/14 time: 0.420853

Epoch: 15/20...
--- Train loss: 0.5467  time: 1.081618
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.15 time: 0.402458
--- Valid loss: 0.5461  time: 0.207285 min loss: 0.5461 epochs since: 0

Epoch: 16/20...
--- Train loss: 0.5426  time: 1.062056
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.16 time: 0.410654
--- Valid loss: 0.5446  time: 0.214528 min loss: 0.5446 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/16 time: 0.403556

Epoch: 17/20...
--- Train loss: 0.5396  time: 1.109497
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.17 time: 0.467383
--- Valid loss: 0.5406  time: 0.21106 min loss: 0.5406 epochs since: 0

Epoch: 18/20...
--- Train loss: 0.5369  time: 1.087418
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.18 time: 0.454381
--- Valid loss: 0.5376  time: 0.221686 min loss: 0.5376 epochs since: 0
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/18 time: 0.528206

Epoch: 19/20...
--- Train loss: 0.5343  time: 1.090064
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/min_valid.19 time: 0.47751
--- Valid loss: 0.5358  time: 0.22055 min loss: 0.5358 epochs since: 0

Epoch: 20/20...
--- Train loss: 0.5332  time: 1.08739
--- Valid loss: 0.5388  time: 0.226004 min loss: 0.5358 epochs since: 1
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/20 time: 0.506333
-------- Saving weights: /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny/weights/20 time: 0.431723
Done training. Wrote to /shared/bms20/projects/GenoCAE/ae_out/ae.M1.ex3.b_0_4.HumanOrigins249_tiny

@bschilder bschilder mentioned this issue Jun 23, 2022
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