EMAN2.3 installation fails on cluster

chr...@caltech.edu

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May 1, 2019, 3:20:17 PM5/1/19

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Hi,

EMAN2.3 installation fails on a cluster computer running RHEL 6.10. To install, I typed 'bash eman2.3.linux64.sh' and specified a different installation location. Below is the full output from the installation.

I also tried installing the latest (today) continuous build, but it also fails with the same error message. EMAN2.22 installation works fine on the other hand. Any idea how to fix this? Thanks in advance.

Best,

Georges

OUTPUT:

installing: python-2.7.16-h9bab390_0 ...

Python 2.7.16 :: Anaconda, Inc.

installing: asn1crypto-0.24.0-py27_0 ...

installing: backports-1.0-py27_1 ...

installing: backports.functools_lru_cache-1.5-py27_1 ...

installing: beautifulsoup4-4.7.1-py27_1 ...

installing: bzip2-1.0.6-h14c3975_5 ...

installing: ca-certificates-2019.1.23-0 ...

installing: certifi-2019.3.9-py27_0 ...

installing: cffi-1.12.3-py27h2e261b9_0 ...

installing: chardet-3.0.4-py27_1 ...

installing: conda-4.6.14-py27_0 ...

installing: conda-build-3.17.8-py27_0 ...

installing: contextlib2-0.5.5-py27hbf4c468_0 ...

installing: cryptography-2.6.1-py27h1ba5d50_0 ...

installing: enum34-1.1.6-py27_1 ...

installing: filelock-3.0.10-py27_0 ...

installing: futures-3.2.0-py27_0 ...

installing: glob2-0.6-py27_1 ...

installing: gsl-2.4-h14c3975_4 ...

installing: icu-58.2-h9c2bf20_1 ...

installing: idna-2.8-py27_0 ...

installing: ipaddress-1.0.22-py27_0 ...

installing: jinja2-2.10.1-py27_0 ...

installing: libarchive-3.3.3-h5d8350f_5 ...

installing: libedit-3.1.20181209-hc058e9b_0 ...

installing: libffi-3.2.1-hd88cf55_4 ...

installing: libgcc-ng-8.2.0-hdf63c60_1 ...

installing: libgfortran-ng-7.3.0-hdf63c60_0 ...

installing: liblief-0.9.0-h7725739_2 ...

installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...

installing: libxml2-2.9.9-he19cac6_0 ...

installing: lz4-c-1.8.1.2-h14c3975_0 ...

installing: lzo-2.10-h49e0be7_2 ...

installing: markupsafe-1.1.1-py27h7b6447c_0 ...

installing: ncurses-6.1-he6710b0_1 ...

installing: openssl-1.1.1b-h7b6447c_1 ...

installing: patchelf-0.9-he6710b0_3 ...

installing: pip-19.0.3-py27_0 ...

installing: pkginfo-1.5.0.1-py27_0 ...

installing: psutil-5.6.1-py27h7b6447c_0 ...

installing: py-lief-0.9.0-py27h7725739_2 ...

installing: pycosat-0.6.3-py27h14c3975_0 ...

installing: pycparser-2.19-py27_0 ...

installing: pyopenssl-19.0.0-py27_0 ...

installing: pysocks-1.6.8-py27_0 ...

installing: python-libarchive-c-2.8-py27_6 ...

installing: pytz-2019.1-py_0 ...

installing: pyyaml-5.1-py27h7b6447c_0 ...

installing: readline-7.0-h7b6447c_5 ...

installing: requests-2.21.0-py27_0 ...

installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...

installing: scandir-1.10.0-py27h7b6447c_0 ...

installing: setuptools-41.0.0-py27_0 ...

installing: six-1.12.0-py27_0 ...

installing: soupsieve-1.8-py27_0 ...

installing: sqlite-3.28.0-h7b6447c_0 ...

installing: tk-8.6.8-hbc83047_0 ...

installing: tqdm-4.31.1-py27_1 ...

installing: urllib3-1.24.1-py27_0 ...

installing: wheel-0.33.1-py27_0 ...

installing: xz-5.2.4-h14c3975_4 ...

installing: yaml-0.1.7-had09818_2 ...

installing: zlib-1.2.11-h7b6447c_3 ...

installing: zstd-1.3.7-h0b5b093_0 ...

installing: eman2-2.3-h6bb024c_0 ...

set: Variable name must begin with a letter.

ERROR: executing post_install.sh failed

Steve Ludtke

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May 1, 2019, 4:29:25 PM5/1/19

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What is the location you specified?

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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Gajiwala, Ketan

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May 1, 2019, 4:47:01 PM5/1/19

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Steve – this is identical to the error message we got, and posted a question about on 4/29/2019, 10:06 am (PDT). - Ketan

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Steve Ludtke

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May 1, 2019, 5:02:54 PM5/1/19

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Yes, I understand. We are trying to track down what might be going on. If you used a non-default path, that's really the only input you give the program, so I'm collecting information. We sorted out the Mac related problem yesterday. This one is trickier...

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

shadow walker

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May 1, 2019, 5:35:10 PM5/1/19

to em...@googlegroups.com, Yee, Jack

Running the installation command with some extra arguments might help us identify the problem.

bash -xv eman2.3.linux64.sh

You can post the output here or you can send it to me privately, in case you are concerned about the information printed.

A workaround could be to skip running post-install scripts and install eman-deps manually.

bash eman2.3.linux64.sh -s

conda install eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y

shadow_walker

shadow walker

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May 1, 2019, 6:31:52 PM5/1/19

to Yee, Jack, em...@googlegroups.com

Is your shell csh? What is the output of "echo $SHELL"?

On Wed, May 1, 2019 at 5:15 PM Yee, Jack <Jack...@pfizer.com> wrote:

Please see attachment.

Thanks

-Jack

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shadow_walker

Steve Ludtke

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May 1, 2019, 8:17:01 PM5/1/19

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Ok, I just did an installation on a CentOS 7.1 and another CentOS 6.5 cluster head node, and both installations went fine. Tunay's suspicions seem to be running towards something going wrong in accounts with a default shell other than bash.

Is anyone who is experiencing installation failure on Linux using an account with /bin/bash set as the default shell, and nothing else odd in their shell configuration?

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

On May 1, 2019, at 2:20 PM, chr...@caltech.edu wrote:

chr...@caltech.edu

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May 1, 2019, 8:30:44 PM5/1/19

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The location I specified was in my home directory on the cluster: /data/work/chreifi/EMAN2.

It looks like you may be correct, the default shell in my account is not bash.

I tried skipping the post-install scripts and install eman-deps manually, which seems to work.

Georges

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Steve Ludtke

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May 1, 2019, 9:28:30 PM5/1/19

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Ok, Tunay has confirmed that the current version of the post-install script is a bash script, but it seems to use whatever you have set as $SHELL. So, the quick fix is eithe, as Georges did, to do the post-install manually, or (untested) modifying SHELL before running the installer.

Tunay is looking into fixing the script and replacing the 2.3 installer download. The software would be identical, it would just be a modified installation script.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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Gajiwala, Ketan

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May 2, 2019, 2:45:30 PM5/2/19

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Thank you, Steve. We now have been able to install 2.3 too. - Ketan

Steve Ludtke

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May 2, 2019, 2:47:56 PM5/2/19

to em...@googlegroups.com, Yee, Jack

Thanks for reporting! We have replaced the binaries on the site with a slightly modified package which shouldn't get angry with non-bash users. If anyone experiences problems with the Linux installer (or any of the others, of course), please don't be shy about reporting it!

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>   Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology   (www.bcm.edu/biochem)
Academic Director, CryoEM Core   (cryoem.bcm.edu)
Co-Director CIBR Center   (www.bcm.edu/research/cibr)

Trushar Patel

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Oct 3, 2019, 6:09:04 PM10/3/19

to EMAN2

Hi everyone, I am pretty new here.

I am having the same issue. See below.

I also tried eman2.31_sphire1.3_huge.linux64, no luck.

==

trushar@trushar-Precision-Tower-3620:~/Documents$ sh eman2.31_sphire1.3.linux64.sh

Welcome to EMAN2 2.31

EMAN2 will now be installed into this location:
/home/trushar/EMAN2

- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below

[/home/trushar/EMAN2] >>>
PREFIX=/home/trushar/EMAN2
installing: python-2.7.16-h9bab390_7 ...
Python 2.7.16 :: Anaconda, Inc.
installing: _libgcc_mutex-0.1-main ...
installing: ca-certificates-2019.8.28-0 ...
installing: libgfortran-ng-7.3.0-hdf63c60_0 ...
installing: libstdcxx-ng-9.1.0-hdf63c60_0 ...
installing: libgcc-ng-9.1.0-hdf63c60_0 ...
installing: bzip2-1.0.8-h7b6447c_0 ...
installing: gsl-2.4-h14c3975_4 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: liblief-0.9.0-h7725739_2 ...

installing: lz4-c-1.8.1.2-h14c3975_0 ...
installing: lzo-2.10-h49e0be7_2 ...

installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1d-h7b6447c_2 ...
installing: patchelf-0.9-he6710b0_3 ...

installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...

installing: libedit-3.1.20181209-hc058e9b_0 ...
installing: libxml2-2.9.9-hea5a465_1 ...
installing: readline-7.0-h7b6447c_5 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: zstd-1.3.7-h0b5b093_0 ...
installing: libarchive-3.3.3-h5d8350f_5 ...
installing: sqlite-3.29.0-h7b6447c_0 ...
installing: eman2-2.31-h6bb024c_0 ...
installing: asn1crypto-0.24.0-py27_0 ...
installing: backports-1.0-py_2 ...
installing: certifi-2019.9.11-py27_0 ...
installing: chardet-3.0.4-py27_1003 ...
installing: contextlib2-0.6.0-py_0 ...
installing: enum34-1.1.6-py27_1 ...
installing: filelock-3.0.12-py_0 ...
installing: futures-3.3.0-py27_0 ...
installing: glob2-0.7-py_0 ...

installing: idna-2.8-py27_0 ...
installing: ipaddress-1.0.22-py27_0 ...

installing: markupsafe-1.1.1-py27h7b6447c_0 ...
installing: pkginfo-1.5.0.1-py27_0 ...
installing: psutil-5.6.3-py27h7b6447c_0 ...

installing: py-lief-0.9.0-py27h7725739_2 ...
installing: pycosat-0.6.3-py27h14c3975_0 ...
installing: pycparser-2.19-py27_0 ...

installing: pysocks-1.7.1-py27_0 ...
installing: python-libarchive-c-2.8-py27_13 ...
installing: pytz-2019.2-py_0 ...
installing: pyyaml-5.1.2-py27h7b6447c_0 ...

installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...
installing: scandir-1.10.0-py27h7b6447c_0 ...

installing: six-1.12.0-py27_0 ...
installing: tqdm-4.36.1-py_0 ...
installing: cffi-1.12.3-py27h2e261b9_0 ...
installing: setuptools-41.2.0-py27_0 ...
installing: backports.functools_lru_cache-1.5-py_2 ...
installing: cryptography-2.7-py27h1ba5d50_0 ...
installing: jinja2-2.10.1-py27_0 ...
installing: wheel-0.33.6-py27_0 ...
installing: pip-19.2.3-py27_0 ...
installing: pyopenssl-19.0.0-py27_0 ...
installing: soupsieve-1.9.3-py27_0 ...
installing: beautifulsoup4-4.8.0-py27_0 ...
installing: urllib3-1.24.2-py27_0 ...
installing: requests-2.22.0-py27_0 ...

installing: conda-4.6.14-py27_0 ...
installing: conda-build-3.17.8-py27_0 ...

+ source /home/trushar/EMAN2/bin/activate
/home/trushar/EMAN2/pkgs/post_install.sh: 5: /home/trushar/EMAN2/pkgs/post_install.sh: source: not found
ERROR: executing post_install.sh failed
==

What should I do?

Thank you!

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Steve Ludtke

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Oct 3, 2019, 6:35:42 PM10/3/19

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Hi Trushar,

please try running the installer with 'bash' not 'sh'. Not positive that will fix it, but it's a first guess...

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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Trushar Patel

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Oct 3, 2019, 6:38:00 PM10/3/19

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Thanks Steven. Will do tomorrow morning. Trushar

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shadow walker

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Oct 3, 2019, 8:05:29 PM10/3/19

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Can you share the logs in /home/trushar/EMAN2/install_logs/? You can send them privately, if you want?

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAF8H0rHVo6%3DN0w8Se_OAu%2BYsowAfw90sd%2BW1Nm6nr%3DxyG8xhYQ%40mail.gmail.com.