Installation problem

Scott Stagg

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Aug 24, 2018, 5:45:14 PM8/24/18

to EMAN2

Hi all,

I am having trouble EMAN2.22. I hate bothering you with problems like this, but I can't figure it out. I followed the instructions, and did the default binary install. I unset any PYTHONPATH, LD, etc, etc and put the bin directory in my path. The e2version.py test worked OK, but I get this error with the speedtest.

[sstagg@hpc-login-24 local]$ e2speedtest.py

Traceback (most recent call last):

File "/gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/e2speedtest.py", line 36, in <module>

from past.utils import old_div

ImportError: No module named past.utils

Any help on this would be greatly appreciated.

Thanks,

Scott

shadow walker

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Aug 24, 2018, 11:19:30 PM8/24/18

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Hi Scott,

It looks like you have a missing dependency which should be resolved by installing the dependency. But, before doing that can you share the output from the following commands to help us diagnose if there is a problem with the binary.

e2version.py

conda info -a

conda list

After that, install the dependency with this command.

conda install future -c defaults

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Scott Stagg

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Aug 24, 2018, 11:41:07 PM8/24/18

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OK. Here are the results of executing your suggestions:

[sstagg@spear-2 EMAN2-22]$ e2version.py

EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )

Your EMAN2 is running on: Linux-3.10.0-693.el7.x86_64-x86_64-with-centos-7.4.1708-Core 3.10.0-693.el7.x86_64

Your Python version is: 2.7.15

[sstagg@spear-2 EMAN2-22]$ e2speedtest.py

Traceback (most recent call last):

File "/gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/e2speedtest.py", line 36, in <module>

from past.utils import old_div

ImportError: No module named past.utils

[sstagg@spear-2 EMAN2-22]$ conda info -a

active environment : None

user config file : /gpfs/home/sstagg/.condarc

populated config files :

conda version : 4.5.10

conda-build version : 3.13.0

python version : 2.7.15.final.0

base environment : /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22 (writable)

channel URLs : https://repo.anaconda.com/pkgs/main/linux-64

https://repo.anaconda.com/pkgs/main/noarch

https://repo.anaconda.com/pkgs/free/linux-64

https://repo.anaconda.com/pkgs/free/noarch

https://repo.anaconda.com/pkgs/r/linux-64

https://repo.anaconda.com/pkgs/r/noarch

https://repo.anaconda.com/pkgs/pro/linux-64

https://repo.anaconda.com/pkgs/pro/noarch

package cache : /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/pkgs

/gpfs/home/sstagg/.conda/pkgs

envs directories : /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/envs

/gpfs/home/sstagg/.conda/envs

platform : linux-64

user-agent : conda/4.5.10 requests/2.19.1 CPython/2.7.15 Linux/3.10.0-693.el7.x86_64 centos/7 glibc/2.17

UID:GID : 700:700

netrc file : None

offline mode : False

# conda environments:

#

base * /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22

sys.version: 2.7.15 |Anaconda, Inc.| (default, May 1...

sys.prefix: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22

sys.executable: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/python

conda location: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/lib/python2.7/site-packages/conda

conda-build: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-build

conda-convert: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-convert

conda-develop: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-develop

conda-env: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-env

conda-index: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-index

conda-inspect: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-inspect

conda-metapackage: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-metapackage

conda-render: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-render

conda-skeleton: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/conda-skeleton

user site dirs:

CIO_TEST: <not set>

CONDA_ROOT: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22

CPATH: /gpfs/research/software/hpc/gnu/include:/panfs/storage.local/opt/hpc/gnu/include:/opt/hpc/gnu/include

LD_LIBRARY_PATH: /gpfs/research/software/hpc/gnu/lib64:/panfs/storage.local/opt/hpc/gnu/lib64:/opt/hpc/gnu/lib64:/opt/hpc/gnu/lib64/netcdf-3

MANPATH: /gpfs/research/software/hpc/gnu/share/man:/panfs/storage.local/opt/hpc/gnu/share/man:/opt/hpc/gnu/share/man:

MATLABPATH: /gpfs/research/software/matlab/toolbox/current/mexnc:/gpfs/research/software/matlab/toolbox/current/snctools

MODULEPATH: /usr/share/Modules/modulefiles:/etc/modulefiles

PATH: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin:/gpfs/research/software/matlab/r2017a/bin:/gpfs/research/software/hpc/gnu/bin:/panfs/storage.local/opt/hpc/gnu/bin:/opt/hpc/gnu/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin

PKG_CONFIG_PATH: /opt/hpc/gnu/lib64/pkgconfig

QT_PLUGIN_PATH: /usr/lib64/kde4/plugins:/usr/lib/kde4/plugins

REQUESTS_CA_BUNDLE: <not set>

SSL_CERT_FILE: <not set>

WARNING: could not import _license.show_info

# try:

# $ conda install -n root _license

[sstagg@spear-2 EMAN2-22]$ conda list

# packages in environment at /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22:

#

# Name Version Build Channel

asn1crypto 0.24.0 py27_0

beautifulsoup4 4.6.3 py27_0

ca-certificates 2018.03.07 0

certifi 2018.8.13 py27_0

cffi 1.11.5 py27h9745a5d_0

chardet 3.0.4 py27_1

conda 4.5.10 py27_0

conda-build 3.13.0 py27_0

conda-env 2.6.0 1

contextlib2 0.5.5 py27hbf4c468_0

cryptography 2.3 py27hb7f436b_0

cryptography-vectors 2.3 py27_0

eman2 2.22 h6bb024c_0 file://home/eman2/anaconda2/conda-bld

enum34 1.1.6 py27_1

filelock 3.0.4 py27_0

futures 3.2.0 py27_0

glob2 0.6 py27_0

gsl 2.4 h14c3975_4

idna 2.7 py27_0

ipaddress 1.0.22 py27_0

jinja2 2.10 py27_0

libedit 3.1.20170329 h6b74fdf_2

libffi 3.2.1 hd88cf55_4

libgcc-ng 8.2.0 hdf63c60_1

libgfortran-ng 7.3.0 hdf63c60_0

libstdcxx-ng 8.2.0 hdf63c60_1

markupsafe 1.0 py27h14c3975_1

ncurses 6.1 hf484d3e_0

openssl 1.0.2p h14c3975_0

patchelf 0.9 hf484d3e_2

pip 10.0.1 py27_0

pkginfo 1.4.2 py27_1

psutil 5.4.6 py27h14c3975_0

pycosat 0.6.3 py27h14c3975_0

pycparser 2.18 py27_1

pyopenssl 18.0.0 py27_0

pysocks 1.6.8 py27_0

python 2.7.15 h1571d57_0

pyyaml 3.13 py27h14c3975_0

readline 7.0 ha6073c6_4

requests 2.19.1 py27_0

ruamel_yaml 0.15.46 py27h14c3975_0

scandir 1.9.0 py27h14c3975_0

setuptools 40.0.0 py27_0

six 1.11.0 py27_1

sqlite 3.24.0 h84994c4_0

tk 8.6.7 hc745277_3

urllib3 1.23 py27_0

wheel 0.31.1 py27_0

xz 5.2.4 h14c3975_4

yaml 0.1.7 had09818_2

zlib 1.2.11 ha838bed_2

[sstagg@spear-2 EMAN2-22]$ conda install future -c defaults

Solving environment: done

## Package Plan ##

environment location: /gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22

added / updated specs:

- future

The following packages will be downloaded:

package | build

---------------------------|-----------------

future-0.16.0 | py27_1 641 KB

The following NEW packages will be INSTALLED:

future: 0.16.0-py27_1

Proceed ([y]/n)?

Downloading and Extracting Packages

future-0.16.0 | 641 KB | ############################################################################################## | 100%

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

[sstagg@spear-2 EMAN2-22]$

[sstagg@spear-2 EMAN2-22]$ e2speedtest.py

Traceback (most recent call last):

File "/gpfs/research/stagg/software/rhel61/usr/local/EMAN2-22/bin/e2speedtest.py", line 44, in <module>

from numpy import array

ImportError: No module named numpy

[sstagg@spear-2 EMAN2-22]$ e2version.py

EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )

Your EMAN2 is running on: Linux-3.10.0-693.el7.x86_64-x86_64-with-centos-7.4.1708-Core 3.10.0-693.el7.x86_64

Your Python version is: 2.7.15

It seems like something isn't getting set up right in the environment.

shadow walker

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Aug 25, 2018, 5:26:23 AM8/25/18

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Most of the dependencies are missing. They are installed automatically at the end of the binary installation. Was your installation interrupted before the last step completed? You can run that step manually.

conda install eman-deps=13.2 -c cryoem -c defaults -c conda-forge -y

Scott Stagg

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Aug 25, 2018, 10:10:08 AM8/25/18

to EMAN2

That worked. The tests all complete successfully now. Thanks for you help!

FYI, my installation was not interrupted. I tried it several times, and it always produced the same results. I think there might be a problem with the installer. I

Mario Borgnia

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May 13, 2019, 10:40:17 AM5/13/19

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I am having a similar problem in version 2.3 for win64

Steve Ludtke

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May 13, 2019, 12:52:19 PM5/13/19

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Hi Mario,

On most machines, this error indicates the need to:

conda install future

However, on Win10, we have seen a number of cases where this is due to another python interpreter installed under Win10 (by some other software package), which is set up to be THE python interpreter for the machine, and it seems that even if a path is set pointing at the EMAN2 Anaconda folder, it is still using the wrong Python interpreter. I'm not enough of a Win10 expert to know if there is a viable solution to this problem (other than uninstalling the conflicting package). It may be that using the embedded ubuntu environment would solve the problem (in a very different way). If you develop any insights, we'd be happy to hear them. The native Win10 system does work on many windows machines, so the problem definitely seems to be one of conflicting installations :^(

--------------------------------------------------------------------------------------

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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Mario Borgnia

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May 13, 2019, 12:54:53 PM5/13/19

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Hi Steve,

Thanks for the quick response. I'll try my best inn the next few hours. I'll let you know if I get any wise(r).

Best

Mario

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/4AE1B66A-A4BA-4C1B-A520-55C14AF7B674%40gmail.com.

Mario Borgnia

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May 16, 2019, 6:11:30 PM5/16/19

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Hi Steve,

I have been trying to install the newest version of EMAN2 (2.33) and the previous one on several platforms with mixed results.

I expected a gradation of issues from WIndows to Linux, but unfortunately I am even having problems on Linux:

Here are the problems I see on 2.22

usuario@TOSHIBA-LINUX:~$ bash ~/Descargas/eman2.22.linux64.sh

Welcome to EMAN2 2.22

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

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

[/home/usuario/EMAN2] >>> /home/usuario/EMAN2.22
PREFIX=/home/usuario/EMAN2.22
installing: python-2.7.15-h1571d57_0 ...
Python 2.7.15 :: Anaconda, Inc.
installing: asn1crypto-0.24.0-py27_0 ...
installing: beautifulsoup4-4.6.3-py27_0 ...
installing: ca-certificates-2018.03.07-0 ...
installing: certifi-2018.8.13-py27_0 ...
installing: cffi-1.11.5-py27h9745a5d_0 ...
installing: chardet-3.0.4-py27_1 ...
installing: conda-4.5.10-py27_0 ...
installing: conda-build-3.13.0-py27_0 ...
installing: conda-env-2.6.0-1 ...
installing: contextlib2-0.5.5-py27hbf4c468_0 ...
installing: cryptography-2.3-py27hb7f436b_0 ...
installing: cryptography-vectors-2.3-py27_0 ...
installing: enum34-1.1.6-py27_1 ...
installing: filelock-3.0.4-py27_0 ...
installing: futures-3.2.0-py27_0 ...
installing: glob2-0.6-py27_0 ...
installing: gsl-2.4-h14c3975_4 ...
installing: idna-2.7-py27_0 ...
installing: ipaddress-1.0.22-py27_0 ...
installing: jinja2-2.10-py27_0 ...
installing: libedit-3.1.20170329-h6b74fdf_2 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libgfortran-ng-7.3.0-hdf63c60_0 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: markupsafe-1.0-py27h14c3975_1 ...
installing: ncurses-6.1-hf484d3e_0 ...
installing: openssl-1.0.2p-h14c3975_0 ...
installing: patchelf-0.9-hf484d3e_2 ...
installing: pip-10.0.1-py27_0 ...
installing: pkginfo-1.4.2-py27_1 ...
installing: psutil-5.4.6-py27h14c3975_0 ...
installing: pycosat-0.6.3-py27h14c3975_0 ...
installing: pycparser-2.18-py27_1 ...
installing: pyopenssl-18.0.0-py27_0 ...
installing: pysocks-1.6.8-py27_0 ...
installing: pyyaml-3.13-py27h14c3975_0 ...
installing: readline-7.0-ha6073c6_4 ...
installing: requests-2.19.1-py27_0 ...
installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...
installing: scandir-1.9.0-py27h14c3975_0 ...
installing: setuptools-40.0.0-py27_0 ...
installing: six-1.11.0-py27_1 ...
installing: sqlite-3.24.0-h84994c4_0 ...
installing: tk-8.6.7-hc745277_3 ...
installing: urllib3-1.23-py27_0 ...
installing: wheel-0.31.1-py27_0 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-ha838bed_2 ...
installing: eman2-2.22-h6bb024c_0 ...

     active environment : base
    active env location : /home/usuario/EMAN2.22
            shell level : 1
       user config file : /home/usuario/.condarc

populated config files :
          conda version : 4.5.10
    conda-build version : 3.13.0
         python version : 2.7.15.final.0

base environment : /home/usuario/EMAN2.22 (writable)

           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch

          package cache : /home/usuario/EMAN2.22/pkgs
                          /home/usuario/.conda/pkgs
       envs directories : /home/usuario/EMAN2.22/envs
                          /home/usuario/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.10 requests/2.19.1 CPython/2.7.15 Linux/4.15.0-47-generic ubuntu/18.04 glibc/2.27
                UID:GID : 1000:1000

netrc file : None
offline mode : False

# conda environments:
#

/home/usuario/EMAN2
base * /home/usuario/EMAN2.22

sys.version: 2.7.15 |Anaconda, Inc.| (default, May 1...

sys.prefix: /home/usuario/EMAN2.22
sys.executable: /home/usuario/EMAN2.22/bin/python
conda location: /home/usuario/EMAN2.22/lib/python2.7/site-packages/conda
conda-build: /home/usuario/EMAN2.22/bin/conda-build
conda-convert: /home/usuario/EMAN2.22/bin/conda-convert
conda-develop: /home/usuario/EMAN2.22/bin/conda-develop
conda-env: /home/usuario/EMAN2.22/bin/conda-env
conda-index: /home/usuario/EMAN2.22/bin/conda-index
conda-inspect: /home/usuario/EMAN2.22/bin/conda-inspect
conda-metapackage: /home/usuario/EMAN2.22/bin/conda-metapackage
conda-render: /home/usuario/EMAN2.22/bin/conda-render
conda-skeleton: /home/usuario/EMAN2.22/bin/conda-skeleton
user site dirs:

ALL_PROXY: <set>
CIO_TEST: <not set>
CONDA_DEFAULT_ENV: base
CONDA_EXE: /home/usuario/EMAN2.22/bin/conda
CONDA_PREFIX: /home/usuario/EMAN2.22
CONDA_PROMPT_MODIFIER: (base)
CONDA_PYTHON_EXE: /home/usuario/EMAN2.22/bin/python
CONDA_ROOT: /home/usuario/EMAN2.22
CONDA_SHLVL: 1
DEFAULTS_PATH: /usr/share/gconf/ubuntu.default.path
FTP_PROXY: <set>
HTTPS_PROXY: <set>
HTTP_PROXY: <set>
MANDATORY_PATH: /usr/share/gconf/ubuntu.mandatory.path
NO_PROXY: <set>
OLD_LD_LIBRARY_PATH: /home/usuario/imagic/lib/:
PATH: /home/usuario/EMAN2.22/bin:/home/usuario/imagic/openmpi/bin:/usr/local/xdsme-master/bin/noarch:/usr/local/sfrmtools:/usr/local/albula/bin:/usr/local/hkl2map/hkl2map-0.4.c-beta:/usr/local/pymol:/usr/local/H5ToXds_1.1.0_x86_64:/usr/local/xds/XDS-INTEL64_Linux_x86_64:/usr/local/buster/MakeTNT/bin:/usr/local/buster/autoBUSTER/bin/linux64:/usr/local/buster/scripts:/usr/local/ccp4/arp_warp_8.0/bin/bin-x86_64-Linux:/usr/local/ccp4/ccp4-7.0/etc:/usr/local/ccp4/ccp4-7.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/usr/local/shelx
REQUESTS_CA_BUNDLE: <not set>
SSL_CERT_FILE: /usr/local/ccp4/ccp4-7.0/etc/ssl/cacert.pem
WINDOWPATH: 2
all_proxy: <set>
ftp_proxy: <set>
http_proxy: <set>
https_proxy: <set>
no_proxy: <set>

WARNING: could not import _license.show_info
# try:
# $ conda install -n root _license

# packages in environment at /home/usuario/EMAN2.22:

Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
- eman-deps=13.2
Use "conda info <package>" to see the dependencies for each package.

INSTALLATION IS NOW COMPLETE

Please, go to http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda
for detailed installation instructions, testing and troubleshooting information.
If this installation is on a Linux cluster,
you will require additional steps before installation is complete!

installation finished.
Do you wish the installer to prepend the EMAN2 install location
to PATH in your /home/usuario/.bashrc ? [yes|no]
[no] >>> no

You may wish to edit your .bashrc to prepend the EMAN2 install location to PATH:

export PATH=/home/usuario/EMAN2.22/bin:$PATH

Thank you for installing EMAN2!
usuario@TOSHIBA-LINUX:~$ vi ~/eman-2.22.bashrc
usuario@TOSHIBA-LINUX:~$ source eman-2.22.bashrc
usuario@TOSHIBA-LINUX:~$ e2version.py

EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )

Your EMAN2 is running on: Linux-4.15.0-47-generic-x86_64-with-debian-buster-sid 4.15.0-47-generic

Your Python version is: 2.7.15

usuario@TOSHIBA-LINUX:~$ e2speedtest.py

Traceback (most recent call last):

File "/home/usuario/EMAN2.22/bin/e2speedtest.py", line 36, in <module>

from past.utils import old_div
ImportError: No module named past.utils

usuario@TOSHIBA-LINUX:~$ conda install eman-deps=13.2 -c cryoem -c defaults -c conda-forge -y
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
- eman-deps=13.2
Use "conda info <package>" to see the dependencies for each package.

usuario@TOSHIBA-LINUX:~$

On Friday, August 24, 2018 at 6:45:14 PM UTC-3, Scott Stagg wrote:

Mario Borgnia

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May 16, 2019, 6:18:44 PM5/16/19

to EMAN2

On 2.33 I have the following problem:

usuario@TOSHIBA-LINUX:~$ source eman.bashrc

usuario@TOSHIBA-LINUX:~$ e2speedtest.py
Traceback (most recent call last):

File "/home/usuario/EMAN2/bin/e2speedtest.py", line 46, in <module>
    from EMAN2 import *
File "/home/usuario/EMAN2/lib/python2.7/site-packages/EMAN2.py", line 51, in <module>
    from EMAN2_cppwrap import *
File "/home/usuario/EMAN2/lib/python2.7/site-packages/EMAN2_cppwrap.py", line 35, in <module>
    from libpyAligner2 import *
ImportError: libboost_python.so.1.63.0: cannot open shared object file: No such file or directory
usuario@TOSHIBA-LINUX:~$

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Steve Ludtke

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May 16, 2019, 6:19:18 PM5/16/19

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Hi Mario,

1) I would focus on 2.3 rather than 2.22

2) are you sure that EMAN2/bin is the first element in the PATH, and that PYTHONPATH and LD_LIBRARY_PATH aren't set?

3) you could try "conda install future" and see if that fixes it

If none of this helps, the output of "conda list" would help debug.

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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)
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Mario Borgnia

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May 16, 2019, 6:28:53 PM5/16/19

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Hi Steve,

Thanks for the superfast response. I did install both versions (first 2.3) using bashrc to differentiate. That is just because I wanted to get something working. Here are the results of the steps that you indicated.

usuario@TOSHIBA-LINUX:~echo $PATH

/home/usuario/EMAN2/bin:/home/usuario/imagic/openmpi/bin:/usr/local/xdsme-master/bin/noarch:/usr/local/sfrmtools:/usr/local/albula/bin:/usr/local/hkl2map/hkl2map-0.4.c-beta:/usr/local/pymol:/usr/local/H5ToXds_1.1.0_x86_64:/usr/local/xds/XDS-INTEL64_Linux_x86_64:/usr/local/buster/MakeTNT/bin:/usr/local/buster/autoBUSTER/bin/linux64:/usr/local/buster/scripts:/usr/local/ccp4/arp_warp_8.0/bin/bin-x86_64-Linux:/usr/local/ccp4/ccp4-7.0/etc:/usr/local/ccp4/ccp4-7.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/usr/local/shelx

usuario@TOSHIBA-LINUX:~$ echo $LD_LIBRARY_PATH
/home/usuario/imagic/lib/:
usuario@TOSHIBA-LINUX:~$ echo $PYTHONPATH

usuario@TOSHIBA-LINUX:~$ conda install future
Collecting package metadata: done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

- file://home/eman2/anaconda2/conda-bld/linux-64::eman2==2.3=h6bb024c_0
done

# All requested packages already installed.

usuario@TOSHIBA-LINUX:~$ conda list
# packages in environment at /home/usuario/EMAN2:

#
# Name Version Build Channel
asn1crypto 0.24.0 py27_0

backports                 1.0                      py27_1
backports.functools_lru_cache 1.5                      py27_1
beautifulsoup4            4.7.1                    py27_1
blas                      1.0                         mkl
bzip2                     1.0.6                h14c3975_5
ca-certificates           2019.1.23                     0
certifi                   2019.3.9                 py27_0
cffi                      1.12.3           py27h2e261b9_0
chardet                   3.0.4                    py27_1
conda                     4.6.14                   py27_0
conda-build               3.17.8                   py27_0
contextlib2               0.5.5            py27hbf4c468_0
cryptography              2.6.1            py27h1ba5d50_0
eman2                     2.3                  h6bb024c_0    file://home/eman2/anaconda2/conda-bld
enum34                    1.1.6                    py27_1
filelock                  3.0.10                   py27_0
future                    0.17.1                   py27_0
futures                   3.2.0                    py27_0
glob2                     0.6                      py27_1
gsl                       2.4                  h14c3975_4
icu                       58.2                 h9c2bf20_1
idna                      2.8                      py27_0
intel-openmp              2019.3                      199
ipaddress                 1.0.22                   py27_0
jinja2                    2.10.1                   py27_0
libarchive                3.3.3                h5d8350f_5
libedit                   3.1.20181209         hc058e9b_0

libffi                    3.2.1                hd88cf55_4
libgcc-ng                 8.2.0                hdf63c60_1
libgfortran-ng            7.3.0                hdf63c60_0

liblief                   0.9.0                h7725739_2
libstdcxx-ng              8.2.0                hdf63c60_1
libxml2                   2.9.9                he19cac6_0
lz4-c                     1.8.1.2              h14c3975_0
lzo                       2.10                 h49e0be7_2
markupsafe                1.1.1            py27h7b6447c_0
mkl                       2019.3                      199
mkl_fft                   1.0.12           py27ha843d7b_0
mkl_random                1.0.2            py27hd81dba3_0
ncurses                   6.1                  he6710b0_1
numpy                     1.16.3           py27h7e9f1db_0
numpy-base                1.16.3           py27hde5b4d6_0
openssl                   1.1.1b               h7b6447c_1
patchelf                  0.9                  he6710b0_3
pip                       19.0.3                   py27_0
pkginfo                   1.5.0.1                  py27_0
psutil                    5.6.1            py27h7b6447c_0
py-lief                   0.9.0            py27h7725739_2
pycosat                   0.6.3            py27h14c3975_0
pycparser                 2.19                     py27_0
pyopenssl                 19.0.0                   py27_0
pysocks                   1.6.8                    py27_0
python                    2.7.16               h9bab390_0
python-libarchive-c       2.8                      py27_6
pytz                      2019.1                     py_0
pyyaml                    5.1              py27h7b6447c_0
readline                  7.0                  h7b6447c_5
requests                  2.21.0                   py27_0
ruamel_yaml               0.15.46          py27h14c3975_0
scandir                   1.10.0           py27h7b6447c_0
setuptools                41.0.0                   py27_0
six                       1.12.0                   py27_0
soupsieve                 1.8                      py27_0
sqlite                    3.28.0               h7b6447c_0
tk                        8.6.8                hbc83047_0
tqdm                      4.31.1                   py27_1
urllib3                   1.24.1                   py27_0
wheel                     0.33.1                   py27_0

xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2

zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0

usuario@TOSHIBA-LINUX:~$

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shadow walker

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May 16, 2019, 6:41:26 PM5/16/19

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Any chance the installation of the dependencies failed? You can confirm that by looking at the installation log in install_logs. The dependencies list shows that at least boost is missing. Try installing them manually.

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

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Steve Ludtke

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May 16, 2019, 6:42:41 PM5/16/19

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shadow_walker, take a look back through what he sent. He did make attempts with the dependencies.

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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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shadow walker

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May 16, 2019, 6:45:18 PM5/16/19

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That was for 2.22 and eman-deps=13.1.

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Mario Borgnia

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May 16, 2019, 6:53:55 PM5/16/19

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Thanks. That worked for now.

Take note of a few more users in Argentina!

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Steve Ludtke

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May 16, 2019, 6:55:30 PM5/16/19

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Indeed, though 2.22 should still install properly....

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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)
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Mario Borgnia

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May 17, 2019, 2:30:50 PM5/17/19

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Hi Steve,

We managed to troubleshoot the Linux installation. The next issue was under Ubuntu for Windows 10:

We managed to get Xserver to work. The programs e2version.py abnd e2speedtest.py work as well. This error showed up when we tried e2display:

This application failed to start because it could not find or load the Qt platform plugin "xcb"
in "".

Available platform plugins are: eglfs, minimal, minimalegl, offscreen, vnc, xcb.

Reinstalling the application may fix this problem.

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Steve Ludtke

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May 17, 2019, 3:32:38 PM5/17/19

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Hi Mario,

well at least we're making some progress :^). See if this gives any more info:

3

To any future readers who come across this - before you start (dangerously) messing around with symlinks to shared libraries, I strongly suggest that you run
export QT_DEBUG_PLUGINS=1
and then run your failing executable again in the Terminal. Read the actual error message thrown by QT, since none of the above solutions addressed the cause of this error in my case.

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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)
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Julian Ratcliffe

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Oct 7, 2019, 10:42:56 PM10/7/19

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Hi Steve,

Sorry to revive an old thread, but I'm trying to get a fresh installation running through Ubuntu for Windows 10, and am having the same issue mentioned above.

After running

export QT_DEBUG_PLUGINS=1 then e2display.py

I get the following:

QFactoryLoader::QFactoryLoader() checking directory path "/home/jratcliffe/EMAN2/plugins/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/home/jratcliffe/EMAN2/plugins/platforms/libqeglfs.so"
Found metadata in lib /home/jratcliffe/EMAN2/plugins/platforms/libqeglfs.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "eglfs"
        ]
    },
    "className": "QEglFSIntegrationPlugin",
    "debug": false,
    "version": 329990
}


Got keys from plugin meta data ("eglfs")
QFactoryLoader::QFactoryLoader() looking at "/home/jratcliffe/EMAN2/plugins/platforms/libqminimal.so"
Found metadata in lib /home/jratcliffe/EMAN2/plugins/platforms/libqminimal.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "minimal"
        ]
    },
    "className": "QMinimalIntegrationPlugin",
    "debug": false,
    "version": 329990
}


Got keys from plugin meta data ("minimal")
QFactoryLoader::QFactoryLoader() looking at "/home/jratcliffe/EMAN2/plugins/platforms/libqminimalegl.so"
Found metadata in lib /home/jratcliffe/EMAN2/plugins/platforms/libqminimalegl.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "minimalegl"
        ]
    },
    "className": "QMinimalEglIntegrationPlugin",
    "debug": false,
    "version": 329990
}


Got keys from plugin meta data ("minimalegl")
QFactoryLoader::QFactoryLoader() looking at "/home/jratcliffe/EMAN2/plugins/platforms/libqoffscreen.so"
Found metadata in lib /home/jratcliffe/EMAN2/plugins/platforms/libqoffscreen.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "offscreen"
        ]
    },
    "className": "QOffscreenIntegrationPlugin",
    "debug": false,
    "version": 329990
}


Got keys from plugin meta data ("offscreen")
QFactoryLoader::QFactoryLoader() looking at "/home/jratcliffe/EMAN2/plugins/platforms/libqvnc.so"
Found metadata in lib /home/jratcliffe/EMAN2/plugins/platforms/libqvnc.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "vnc"
        ]
    },
    "className": "QVncIntegrationPlugin",
    "debug": false,
    "version": 329990
}


Got keys from plugin meta data ("vnc")
QFactoryLoader::QFactoryLoader() looking at "/home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so"
Found metadata in lib /home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "xcb"
        ]
    },
    "className": "QXcbIntegrationPlugin",
    "debug": false,
    "version": 329990
}


Got keys from plugin meta data ("xcb")
QFactoryLoader::QFactoryLoader() checking directory path "/home/jratcliffe/EMAN2/bin/platforms" ...
Cannot load library /home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so: (libXi.so.6: cannot open shared object file: No such file or directory)
QLibraryPrivate::loadPlugin failed on "/home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so" : "Cannot load library /home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so: (libXi.so.6: cannot open shared object file: No such file or directory)"


This application failed to start because it could not find or load the Qt platform plugin "xcb"
in "".

Available platform plugins are: eglfs, minimal, minimalegl, offscreen, vnc, xcb.

Reinstalling the application may fix this problem.

Aborted (core dumped)

If you have any insights to help me figure this out I would appreciate it.

Cheers,

Julian

Hi Mario,

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Steve Ludtke

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Oct 7, 2019, 10:52:07 PM10/7/19

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Looks like the problem is here:

Cannot load library /home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so: (libXi.so.6: cannot open shared object file: No such file or directory)
QLibraryPrivate::loadPlugin failed on "/home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so" : "Cannot load library /home/jratcliffe/EMAN2/plugins/platforms/libqxcb.so: (libXi.so.6: cannot open shared object file: No such file or directory)"

That is, it cannot find libXi.so.6

--------------------------------------------------------------------------------------
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)

Julian Ratcliffe

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Oct 8, 2019, 1:24:10 AM10/8/19

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Looks like you're right. I installed libxi6 and now everything seems to be working. Thank you

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