Hello,
I am trying to install Psi4 in my project directory on my University’s high-performance computing cluster. I have followed the instructions provided in the sections on detailed installations of Miniconda and Psi4 on your webpage: “http://www.psicode.org/psi4manual/master/conda.html#detailed-installation-of-miniconda”. However, when I try to create a Psi4 environment, I find the following error in the test-job section:
Traceback (most recent call last):
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/inputparser.py”, line 43, in
import pubchem
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/pubchem.py”, line 61, in
from p4util.exceptions import *
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/p4util/init.py”, line 32, in
from .util import *
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/p4util/util.py”, line 32, in
import numpy as np
ImportError: No module named numpy
Is it because the numpy package isn’t linked properly? I see the linking progress to be 56% in the first part of the file. The full output is copied below.
Thank you.
Best regards,
Sharani
[Newton:sigma00 roy]$ conda create -n p4env psi4
Fetching package metadata: …
Solving package specifications: …
Package plan for installation in environment /lustre/projects/roy/miniconda2/envs/p4env:
The following packages will be downloaded:
package | build
---------------------------|-----------------
gsl-1.16 | 1 6.8 MB
mkl-11.3.3 | 0 122.1 MB
ncurses-5.9 | 0 1.4 MB
hdf5-1.8.16 | 0 1.9 MB
pcmsolver-1.1.1 | 3 20.9 MB
numpy-1.11.0 | py27_1 6.2 MB
psi4-1.0rc0 | py27_g15fc63c 54.1 MB
------------------------------------------------------------
Total: 213.4 MB
The following NEW packages will be INSTALLED:
gsl: 1.16-1
hdf5: 1.8.16-0
mkl: 11.3.3-0
ncurses: 5.9-0
numpy: 1.11.0-py27_1
openssl: 1.0.2h-0
pcmsolver: 1.1.1-3
pip: 8.1.1-py27_1
psi4: 1.0rc0-py27_g15fc63c
python: 2.7.11-0
readline: 6.2-2
setuptools: 20.7.0-py27_0
sqlite: 3.9.2-0
tk: 8.5.18-0
wheel: 0.29.0-py27_0
zlib: 1.2.8-0
Proceed ([y]/n)? y
Fetching packages …
gsl-1.16-1.tar 100% |################################| Time: 0:00:00 13.61 MB/s
mkl-11.3.3-0.t 100% |################################| Time: 0:00:05 21.67 MB/s
ncurses-5.9-0. 100% |################################| Time: 0:00:00 4.34 MB/s
hdf5-1.8.16-0. 100% |################################| Time: 0:00:00 4.43 MB/s
pcmsolver-1.1. 100% |################################| Time: 0:00:01 18.28 MB/s
numpy-1.11.0-p 100% |################################| Time: 0:00:00 9.16 MB/s
psi4-1.0rc0-py 100% |################################| Time: 0:00:02 26.76 MB/s
Extracting packages …
[ COMPLETE ]|###################################################| 100%
Linking packages …
[python ]|############################# | 56%
Thank you for installing psi4. Additional resources:
Website: “www.psicode.org”
Inputs: “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/samples”
Manual: “http://psicode.org/psi4manual/master/index.html”
GitHub: “https://github.com/psi4/psi4/wiki”
Binary: “https://anaconda.org/psi4”
Runtime Environment Diagnostic: “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/scripts/setenv.py”
Youtube: “https://www.youtube.com/user/psitutorials”
For csh/tcsh command-line use, add to shell or ~/.tcshrc file:
setenv PATH /lustre/projects/roy/miniconda2/envs/p4env/bin:$PATH
setenv PSI_SCRATCH /path/to/existing/writable/local-not-network/disk/for/scratch/files
For sh/bash command-line use, add to shell or ~/.bashrc file:
export PATH=/lustre/projects/roy/miniconda2/envs/p4env/bin:$PATH
export PSI_SCRATCH=/path/to/existing/writable/local-not-network/disk/for/scratch/files
Report problems at “Report conda update psi4 oddities here”
Traceback (most recent call last):
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/inputparser.py”, line 43, in
import pubchem
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/pubchem.py”, line 61, in
from p4util.exceptions import *
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/p4util/init.py”, line 32, in
from .util import *
File “/lustre/projects/roy/miniconda2/envs/p4env/share/psi4/python/p4util/util.py”, line 32, in
import numpy as np
ImportError: No module named numpy
[ COMPLETE ]|###################################################| 100%
To activate this environment, use:
$ source activate p4env
To deactivate this environment, use:
$ source deactivate