Python issue during installation

pete · January 20, 2023, 1:07am

Any ideas why the installation would be failing with the following error?

Executing transaction: \
/home/cryosparc/cryosparc_master/deps_bundle/python/anaconda.sh: line 436: 193749 Killed
CONDA_SAFETY_CHECKS=disabled CONDA_EXTRA_SAFETY_CHECKS=no CONDA_ROLLBACK_ENABLED=no CONDA_CHANNELS= (URLs removed for posting) CONDA_PKGS_DIRS=“$PREFIX/pkgs” “$CONDA_EXEC” install --offline --file “$PREFIX/pkgs/env.txt” -yp “$PREFIX”
check_install_deps.sh: 66: ERROR: installing python failed.

ping repo.anaconda.com
PING repo.anaconda.com (104.16.131.3) 56(84) bytes of data.
64 bytes from 104.16.131.3 (104.16.131.3): icmp_seq=1 ttl=60 time=11.2 ms

(Removed the anaconda repo URLs to comply with the posting requirements)

wtempel · January 24, 2023, 7:05pm

Please can you post the command that produced the error and then try:

cd /home/cryosparc/cryosparc_master
./bin/cryosparcm forcedeps 2>&1 | tee forcedeps_master_20230124.out

pete · January 28, 2023, 2:48pm

The command used was:

./install.sh --license (removed) --hostname (removed) --dbpath /home/cryosparc/cryosparc_database --port 39000

The output from

cd /home/cryosparc/cryosparc_master
./bin/cryosparcm forcedeps 2>&1 | tee forcedeps_master_20230124.out

  Checking dependencies...
  Forcing dependencies to be reinstalled...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/home/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Extracting : brotlipy-0.7.0-py38h27cfd23_1003.conda:  10%|      9 [00:58<35:23, 58.99s/it]
Extracting : ca-certificat-trust-0.1.1-pyhd3eb1b0_0.conda:  23%|       | 9/39 [00:58<29:29, 58.99s/it]
Extracting : xz-5.2.5-h7b6447c_0.conda:  38%|      | 15/39 [00:5:58<24:34, 58.99s/it]
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda 51%|    | 20/39 [00:58<18:40, 58.99s/it]
Extracting : pysocks-1.7.1-py38h06a4308_0.conda:  67%| | 25/39 [00:58<13:45, 58.99s/it]
Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda:  79%|  | 30/39 [00:58<08:50, 58.99s/it]
Extracting : sqlite-3.38.2-hc218d9a_0.conda:  92%|| 36/39 [00:5:55, 58.99s/it]
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/cryosparc/cryosparc_master/deps/anaconda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py38h27cfd23_1003
    - ca-certificates==2022.3.29=h06a4308_1
    - certifi==2021.10.8=py38h06a4308_2
    - cffi==1.15.0=py38hd667e15_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=py38h7f8727e_0
    - conda==4.12.0=py38h06a4308_0
    - cryptography==36.0.0=py38h9ce1e76_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=py38h06a4308_0
    - pycosat==0.6.3=py38h7b6447c_1
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py38h06a4308_0
    - python==3.8.13=h12debd9_0
    - readline==8.1.2=h7f8727e_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py38h27cfd23_0
    - setuptools==61.2.0=py38h06a4308_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=hc218d9a_0
    - tk==8.6.11=h1ccaba5_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.12=h7f8727e_1


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py38h06a4308_2
  cffi               pkgs/main/linux-64::cffi-1.15.0-py38hd667e15_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-py38h06a4308_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-py38h7f8727e_0
  cryptography       pkgs/main/linux-64::cryptography-36.0.0-py38h9ce1e76_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-py38h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
  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-py38h06a4308_0
  python             pkgs/main/linux-64::python-3.8.13-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py38h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-61.2.0-py38h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1


Preparing transaction: ...working... done
Executing transaction: ...working... /home/cryosparc/cryosparc_master/deps_bundle/python/anaconda.sh: line 436: 119432 Killed
      CONDA_SAFETY_CHECKS=disabled CONDA_EXTRA_SAFETY_CHECKS=no CONDA_ROLLBACK_ENABLED=no CONDA_CHANNELS=  (URLs removed) CONDA_PKGS_DIRS="$PREFIX/pkgs" "$CONDA_EXEC" instal
l --offline --file "$PREFIX/pkgs/env.txt" -yp "$PREFIX"
check_install_deps.sh: 59: ERROR: installing python failed.

wtempel · January 29, 2023, 10:05pm

Thanks. Please can you also post the outputs of:

env | grep -v LICENSE
uname -a
which conda (which may produce no output)
free -g

pete · January 31, 2023, 4:37pm

env | grep -v LICENSE

MANPATH=/opt/lmod/7.7/gcc/lmod/lmod/share/man::
SHELL=/bin/bash
TERM=xterm-256color
HISTSIZE=1000
MODULEPATH_ROOT=/opt/lmod/7.7/gcc/modulefiles
LMOD_PKG=/opt/lmod/7.7/gcc/lmod/lmod
QTDIR=/usr/lib64/qt-3.3
LMOD_SHORT_TIME=86400
LMOD_VERSION=7.7
QTINC=/usr/lib64/qt-3.3/include
QT_GRAPHICSSYSTEM_CHECKED=1
USER=cryo
LMOD_sys=Linux
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
MAIL=/var/spool/mail/cryo
PATH=/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/home/cryo/bin
LMOD_SETTARG_CMD=:
PWD=(exact location removed for security reasons)/cryosparc
LANG=en_US.UTF-8
MODULEPATH=/etc/modulefiles:/opt/modulefiles/Compilers:/opt/modulefiles/Applications
LOADEDMODULES=
KDEDIRS=/usr
LMOD_CMD=/opt/lmod/7.7/gcc/lmod/lmod/libexec/lmod
HISTCONTROL=ignoredups
SHLVL=1
HOME=/home/cryo
BASH_ENV=/opt/lmod/7.7/gcc/lmod/lmod/init/bash
MATHEMATICA_HOME=/opt/mathematica/12.2.0
LOGNAME=cryo
QTLIB=/usr/lib64/qt-3.3/lib
XDG_DATA_DIRS=/home/cryo/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
MODULESHOME=/opt/lmod/7.7/gcc/lmod/lmod
LESSOPEN=||/usr/bin/lesspipe.sh %s
LMOD_FULL_SETTARG_SUPPORT=no
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
LMOD_DIR=/opt/lmod/7.7/gcc/lmod/lmod/libexec
SCRATCH=/scratch/cryo
BASH_FUNC_module()=() {  eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh);
 eval `/opt/lmod/7.7/gcc/lmod/7.7/init/moduleloadlog.sh $*` 2> /dev/null
}
BASH_FUNC_ml()=() {  eval $($LMOD_DIR/ml_cmd "$@");
 eval `/opt/lmod/7.7/gcc/lmod/7.7/init/moduleloadlog.sh $*` 2> /dev/null
}
OLDPWD=(location removed for security reasons)
_=/bin/env

uname -a

Linux (hostname removed for security reasons) 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

which conda

/usr/bin/which: no conda in (/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/home/cryo/bin)

free -g

              total        used        free      shared  buff/cache   available
Mem:             92           7           6           2          78          83
Swap:             3           0           3

wtempel · February 3, 2023, 4:10pm

Unfortunately we do not have any explanation for this error.
Could the problem be security-related:

selinux?
a network- and/or host-based security agent?
an obscure file ownership/permissions issue? (related discussion on stackoverflow)

ff98li · February 14, 2023, 10:23pm

Hi, I have encountered the same error when trying to install CryoSPARC on HPC. It was solved after requesting more RAM allocation. Hopefully this can help you.

AlekS · May 2, 2023, 1:52pm

Hi, I had a similar problem and @ff98li is right, it’s due to memory. I added the argument --mem=0 to the salloc to request all the memory in the node.