Hi Billy,  python 2.6.6 is installed. I am running Sci Linux; should not make a big difference to CentOS. yum gives: Installed Packages python.x86_64 2.6.6-66.el6_8 Best, Guenter

Hi Guenter,

What version of python do you use? The error is saying that the "argparse" module is not available, but it should be available on the default system python for CentOS 6 (python 2.6.x).

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Tue, Feb 12, 2019 at 7:17 AM Guenter Fritz mailto:[email protected]> wrote:

Dear phenix developers,

I get errors trying to install latest builds from 1.14.3405, 3406, 3409  64bit centos6 on Scientific Linux machines still running 6.6 (kernel 2.6.32). 1.14.3395 installed without any problem.

The downloaded file is OK.  1.14.3409 64bit centos6 installed on Ubuntu 18.04 without any problem.

I also tried to install from source but got the same error output (see below). I googeled some error outputs - looks like some python error. Do I have to update finally?

Best regards,

Guenter

Output trying to install from source:

[guenter@msm68 phenix-installer-dev-3409-source]$ ./install --prefix=/home/software/PHENIX/1.14.3409/ --nproc=10 Traceback (most recent call last):   File "./bin/install.py", line 20, in <module>     from libtbx.auto_build import install_distribution   File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_distribution.py", line 75, in <module>     from libtbx.auto_build import install_base_packages   File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module>     from .package_defs import *   File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/package_defs.py", line 18, in <module>     from .bootstrap import Toolbox   File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/bootstrap.py", line 14, in <module>     import argparse ImportError: No module named argparse

Similar from an installer:

[guenter@msm68 phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6]$ ./install --prefix=/home/software/PHENIX/1.14.3405/ Traceback (most recent call last):   File "./bin/install.py", line 20, in <module>     from libtbx.auto_build import install_distribution   File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 75, in <module>     from libtbx.auto_build import install_base_packages   File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module>     from .package_defs import *   File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/package_defs.py", line 18, in <module>     from .bootstrap import Toolbox   File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/bootstrap.py", line 14, in <module>     import argparse ImportError: No module named argparse

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Thanks for letting us know! I thought argparse was installed by default for python 2.6. We have that package installed as well. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Feb 13, 2019 at 4:56 AM Guenter Fritz < [email protected]> wrote:

Hi Billy,

I figured out that argparse has not been part of python installed. Thanks for pointing me to python. Problem is solved by installing argparse: yum install python-argparse

Cheers, guenter

Hi Guenter,

What version of python do you use? The error is saying that the "argparse" module is not available, but it should be available on the default system python for CentOS 6 (python 2.6.x).

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Tue, Feb 12, 2019 at 7:17 AM Guenter Fritz < [email protected]> wrote:

...

Dear phenix developers,

I get errors trying to install latest builds from 1.14.3405, 3406, 3409 64bit centos6 on Scientific Linux machines still running 6.6 (kernel 2.6.32). 1.14.3395 installed without any problem.

The downloaded file is OK. 1.14.3409 64bit centos6 installed on Ubuntu 18.04 without any problem.

I also tried to install from source but got the same error output (see below). I googeled some error outputs - looks like some python error. Do I have to update finally?

Best regards,

Guenter

Output trying to install from source:

[guenter@msm68 phenix-installer-dev-3409-source]$ ./install --prefix=/home/software/PHENIX/1.14.3409/ --nproc=10 Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse

Similar from an installer:

[guenter@msm68 phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6]$ ./install --prefix=/home/software/PHENIX/1.14.3405/ Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse

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