Psi4conda-1.3.2-py37-Linux-x86_64 installation problem

Dear Psi4 Community,

when installing the subject I got the following error:

Psi4conda-1.3.2-py37-Linux-installing: psi4-rt-1.3.2-py37ha6b60c8_0 …
if: Expression Syntax.
then: Command not found.
ERROR: executing post_install.sh failed_64

When trying to run manually after this installation error, it says:
File “/home/leonid/psi4conda/bin/psi4”, line 177, in
import psi4
File “/home/leonid/psi4conda/lib//python3.7/site-packages/psi4/init.py”, line 82, in
from .driver import endorsed_plugins
File “/home/leonid/psi4conda/lib//python3.7/site-packages/psi4/driver/init.py”, line 33, in
from qcelemental import constants
ModuleNotFoundError: No module named ‘qcelemental’

I would appreciate any help.

I defer to @loriab on any errors during a conda installation.

Normally whenever you see a ModuleNotFoundError, a good first idea is to pip install the module it can’t find. qcelemental may be special because the version requirements seem to change frequently.

any chance you weren’t explicitly bashing the installer (i.e., bash Psi4conda-1.3.2...)? there’s a post-install script that moves “noarch” packages like qcelemental into the correct location (details and why upon request), and it’s looking like something very fundamental is going wrong. afaik this post-install step has been working fine for months, so your environment or execution are my first inquires.

I was doing exactly as written here
https://admiring-tesla-08529a.netlify.com/installs/v132/
the installation was successful till the final step. I managed to install an earlier version
psi4conda-1.2.1-py27-Linux-x86_64 as the temporary solution which works fine.

The pip version was “You are using pip version 10.0.1”, so I updated it to 19.2.1, though haven’t tried to install the py37 version of psi4 yet.

let’s get a which conda python psi4, conda list, and psi4 --version, please. did you already have psi4 present by any means (installer/conda/clone) before starting the 1.3.2 installation? I’m wondering if your environment was set up for an older psi and the new psi is trying to run against that older (and for new psi4, incomplete) set of dependencies.

@loriab, hello, i have the same problem with leonidas:
if: Expression Syntax.
ERROR: executing post_install.sh failed
which conda:
/home/401orca/ly/sourcefolders/psi4conda/bin/conda
which python:
/home/401orca/ly/sourcefolders/psi4conda/bin/python
which psi4:
/home/401orca/ly/sourcefolders/psi4conda/bin/psi4
conda list:
# packages in environment at /home/401orca/ly/sourcefolders/psi4conda:
#
# Name Version Build Channel
ambit 0.3 h137fa24_1 psi4
asn1crypto 0.24.0 py36_0
atomicwrites 1.3.0 py36_1
attrs 19.1.0 py36_1
blas 1.0 mkl
ca-certificates 2019.1.23 0
certifi 2019.3.9 py36_0
cffi 1.12.3 py36h2e261b9_0
chardet 3.0.4 py36_1
chemps2 1.8.9 h8c3debe_0 psi4
conda 4.6.14 py36_0
cryptography 2.6.1 py36h1ba5d50_0
cvxopt 1.2.0 py36hfa32c7d_0
dataclasses 0.6 py_0 psi4
decorator 4.4.0 py36_1
deepdiff 3.3.0 py36_1 psi4
dftd3 3.2.1 h84218bc_2 psi4
dkh 1.2 h173d85e_2 psi4
future 0.17.1 py36_0
gau2grid 1.3.1 h035aef0_0 psi4
gcp 2.0.2 h84218bc_1 psi4
gdma 2.2.6 h0e1e685_6 psi4
glpk 4.65 h3ceedfd_2
gmp 6.1.2 h6c8ec71_1
gsl 2.4 h14c3975_4
h5py 2.8.0 py36h989c5e5_3
hdf5 1.10.2 hba1933b_1
idna 2.8 py36_0
intel-openmp 2019.3 199
jsonpickle 0.9.6 py36_0 psi4
libedit 3.1.20181209 hc058e9b_0
libefp 1.5.0 h84097be_1 psi4
libffi 3.2.1 hd88cf55_4
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.3.0 hdf63c60_0
libint 1.2.1 hb4a4fd4_6 psi4
libstdcxx-ng 8.2.0 hdf63c60_1
libxc 4.3.4 h7b6447c_0 psi4
metis 5.1.0 hf484d3e_4
mkl 2019.3 199
mkl_fft 1.0.12 py36ha843d7b_0
mkl_random 1.0.2 py36hd81dba3_0
more-itertools 7.0.0 py36_0
ncurses 6.1 he6710b0_1
networkx 2.3 py_0
numpy 1.16.3 py36h7e9f1db_0
numpy-base 1.16.3 py36hde5b4d6_0
openfermion 0.9 py36hd763080_1 psi4
openfermionpsi4 0.4 py36h934b37d_0 psi4
openssl 1.1.1b h7b6447c_1
pcmsolver 1.2.1 py36h8733eb9_0 psi4
pint 0.9 py36_2 psi4
pip 19.1.1 py36_0
pluggy 0.11.0 py_0
psi4 1.3.2+ecbda83 py36h189457c_0 psi4
psi4-rt 1.3.2 py36ha6b60c8_0 psi4
py 1.8.0 py36_0
pycosat 0.6.3 py36h14c3975_0
pycparser 2.19 py36_0
pydantic 0.23 py36_0 psi4
pylibefp 0.4+f42ffb8 py36h5a86982_1 psi4
pyopenssl 19.0.0 py36_0
pysocks 1.7.0 py36_0
pytest 4.5.0 py36_0
python 3.6.8 h0371630_0
qcelemental 0.4.0 py_0 psi4
readline 7.0 h7b6447c_5
requests 2.21.0 py36_0
resp 0.7 py36ha93d1a2_0 psi4
ruamel_yaml 0.15.46 py36h14c3975_0
scipy 1.2.1 py36h7c811a0_0
setuptools 41.0.1 py36_0
simint 0.7 h642920c_1 psi4
six 1.12.0 py36_0
snsmp2 1.0.3 py36he403277_2 psi4
sqlite 3.28.0 h7b6447c_0
suitesparse 5.2.0 h9e4a6bb_0
tbb 2019.4 hfd86e86_0
tk 8.6.8 hbc83047_0
urllib3 1.24.2 py36_0
v2rdm_casscf 0.8 py36hc3560e4_6 psi4
wcwidth 0.1.7 py36_0
wheel 0.33.4 py36_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zlib 1.2.11 h7b6447c_3
psi4 --version:
Segmentation fault (core dumped)
ldd --version:
ldd (GNU libc) 2.12
Copyright © 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

What/when exactly was the error besides the above?

@loriab, My command line is this:
$ bash Psi4conda-1.3.2-py36-Linux-x86_64.sh -b -p /home/401orca/ly/sourcefolders/psi4conda/

installing: psi4-1.3.2+ecbda83-py36h189457c_0 …

  Thank you for installing Psi4.
    Website: psicode.org
    Forum:   forum.psicode.org
    Manual:  psicode.org/psi4manual/master/index.html
    GitHub:  github.com/psi4/psi4
    Binary:  anaconda.org/psi4/psi4
    Inputs:   /home/401orca/ly/sourcefolders/psi4conda/share/psi4/samples
    Test (after first activating conda installation or environment):
      psi4  /home/401orca/ly/sourcefolders/psi4conda/share/psi4/samples/sapt1/test.in
      psi4 --test

  For csh/tcsh command-line use, add to shell or ~/.tcshrc file:
    source /home/401orca/ly/sourcefolders/psi4conda/etc/profile.d/conda.csh
    conda activate
    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:
    source  /home/401orca/ly/sourcefolders/psi4conda/etc/profile.d/conda.sh
    conda activate
    export PSI_SCRATCH=/path/to/existing/writable/local-not-network/disk/for/scratch/files

installing: snsmp2-1.0.3-py36he403277_2 ...
installing: openfermionpsi4-0.4-py36h934b37d_0 ...
installing: psi4-rt-1.3.2-py36ha6b60c8_0 ...
if: Expression Syntax.
ERROR: executing post_install.sh failed

I don’t know if it install successfully ? My shell is cshell.

Maybe executing this little script failed. Haven’t seen that before, but I’d believe anything of csh. If you cd /home/401orca/ly/sourcefolders/psi4conda && ls and there’s a site-packages/ folder sitting there, try cp -r site-packages/* lib/python3.6/site-packages . Report back which conda python psi4, please.

@loriab, which conda python psi4

/home/401orca/ly/sourcefolders/psi4conda/bin/conda
/home/401orca/ly/sourcefolders/psi4conda/bin/python
/home/401orca/ly/sourcefolders/psi4conda/bin/psi4

psi4 -V

Segmentation fault (core dumped)

ok. what was the result of the cd/ls/cp sequence?

@loriab, I completed it successfully but nothing happened:
$ cd /home/401orca/ly/sourcefolders/psi4conda && ls
bin compiler_compat condabin conda-meta envs etc include lib pkgs share shell site-packages ssl x86_64-conda_cos6-linux-gnu
$ cp -r site-packages/* lib/python3.6/site-packages
$ which conda python psi4
/home/401orca/ly/sourcefolders/psi4conda/bin/conda /home/401orca/ly/sourcefolders/psi4conda/bin/python /home/401orca/ly/sourcefolders/psi4conda/bin/psi4
$ psi4 -V
Segmentation fault (core dumped)

I also try to install the old version from http://vergil.chemistry.gatech.edu/nu-psicode/install-v1.2.html and it install successfully. However, the psi4 still doesn’t work as expect:
$ psi4 -V
Segmentation fault (core dumped)

gdb --args python psi4 share/psi4/samples/tu1-h2o-energy/test.in
(gdb) run
Program received signal SIGSEGV, Segmentation fault.
0x00002aaace047012 in __kmp_register_root () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/../../../libiomp5.so
(gdb) bt
#0  0x00002aaace047012 in __kmp_register_root () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/../../../libiomp5.so
#1  0x00002aaace05251b in _INTERNAL_25_______src_kmp_runtime_cpp_6206a45a::__kmp_do_serial_initialize() ()
   from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/../../../libiomp5.so
#2  0x00002aaace046560 in __kmp_get_global_thread_id_reg () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/../../../libiomp5.so
#3  0x00002aaace034e49 in omp_init_lock@OMP_3.0 () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/../../../libiomp5.so
#4  0x00002aaab360d2ad in psi::timer_init() () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/core.so
#5  0x00002aaab3489326 in psi4_python_module_initialize() () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/core.so
#6  0x00002aaab34870e6 in _ZZN8pybind1112cpp_function10initializeIRPFbvEbJEJNS_4nameENS_5scopeENS_7siblingEEEEvOT_PFT0_DpT1_EDpRKT2_ENUlRNS_6detail13function_callEE_4_FUNESL_ ()
   from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/core.so
#7  0x00002aaab2f3c046 in pybind11::cpp_function::dispatcher(_object*, _object*, _object*) () from /home/401orca/ly/sourcefolders/psi4conda/lib//python3.6/site-packages/psi4/core.so
#8  0x00002aaaaabba9e4 in _PyCFunction_FastCallDict ()
#9  0x00002aaaaac47dfc in call_function ()
#10 0x00002aaaaac6c94a in _PyEval_EvalFrameDefault ()
#11 0x00002aaaaac42cb9 in PyEval_EvalCodeEx ()
#12 0x00002aaaaac43a4c in PyEval_EvalCode ()
#13 0x00002aaaaac6a26d in builtin_exec ()
#14 0x00002aaaaabbdae1 in PyCFunction_Call ()
#15 0x00002aaaaac71aac in _PyEval_EvalFrameDefault ()
#16 0x00002aaaaac41206 in _PyEval_EvalCodeWithName ()
#17 0x00002aaaaac421cf in fast_function ()
#18 0x00002aaaaac47ed5 in call_function ()
#19 0x00002aaaaac6c94a in _PyEval_EvalFrameDefault ()
#20 0x00002aaaaac41f8b in fast_function ()
#21 0x00002aaaaac47ed5 in call_function ()
#22 0x00002aaaaac6c94a in _PyEval_EvalFrameDefault ()
#23 0x00002aaaaac41f8b in fast_function ()
#24 0x00002aaaaac47ed5 in call_function ()
#25 0x00002aaaaac6c94a in _PyEval_EvalFrameDefault ()
#26 0x00002aaaaac41f8b in fast_function ()
#27 0x00002aaaaac47ed5 in call_function ()
#28 0x00002aaaaac6c94a in _PyEval_EvalFrameDefault ()
#29 0x00002aaaaac425db in _PyFunction_FastCallDict ()
#30 0x00002aaaaabbadaf in _PyObject_FastCallDict ()
#31 0x00002aaaaabfe0e0 in _PyObject_CallMethodIdObjArgs ()
#32 0x00002aaaaabb16e0 in PyImport_ImportModuleLevelObject ()
#33 0x00002aaaaac6f38e in _PyEval_EvalFrameDefault ()
#34 0x00002aaaaac42cb9 in PyEval_EvalCodeEx ()
#35 0x00002aaaaac43a4c in PyEval_EvalCode ()
#36 0x00002aaaaacbfc44 in run_mod ()
#37 0x00002aaaaacc0041 in PyRun_FileExFlags ()
#38 0x00002aaaaacc0244 in PyRun_SimpleFileExFlags ()
#39 0x00002aaaaacc3d24 in Py_Main ()
#40 0x00002aaaaab8b75e in main ()

$ ldd libiomp5.so

linux-vdso.so.1 =>  (0x00007fffa2dff000)
libgcc_s.so.1 => /home/chenh/anaconda3/lib/libgcc_s.so.1 (0x00002ad717d27000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ad717f39000)
libc.so.6 => /lib64/libc.so.6 (0x00002ad718157000)
/lib64/ld-linux-x86-64.so.2 (0x00000034fd600000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002ad7184e9000)

I think the libiomp5.so may link a wrong libgcc_s.so.1 which is not in /home/401orca/ly/sourcefolders/psi4conda/lib/.I tried to compile from source code, but found that it needs to be networked. Do you know how to compile without network?

If you don’t mind, how about blowing away the broken psi4conda shell script and installation and trying again from this page (https://admiring-tesla-08529a.netlify.com/installs/v132/). Switch to the bash shell before doing anything. And please paste me the full terminal session.

(I recommend giving the 1.3.2 another try, but you can get 1.2.1 off that same page. Some browsers changed the rules about renaming files during a download, so some psi4conda/Psi4conda conventions got messed up. I suspect that’s what’s going on with the 1.2.x page you linked to.)

@loriab, ok, I deleted the broken psi4conda shell script and installation and donwlonded from https://admiring-tesla-08529a.netlify.com/installs/v132/:
$ bash
$ bash Psi4conda-1.3.2-py36-Linux-x86_64.sh -b -p /home/chenh/ly/sourcefolders/psi4conda

PREFIX=/home/chenh/ly/sourcefolders/psi4conda
installing: python-3.6.8-h0371630_0 ...
Python 3.6.8 :: Anaconda, Inc.
installing: blas-1.0-mkl ...
installing: ca-certificates-2019.1.23-0 ...
installing: dftd3-3.2.1-h84218bc_2 ...
installing: dkh-1.2-h173d85e_2 ...
installing: gcp-2.0.2-h84218bc_1 ...
installing: gdma-2.2.6-h0e1e685_6 ...
installing: intel-openmp-2019.3-199 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libgfortran-ng-7.3.0-hdf63c60_0 ...
installing: libint-1.2.1-hb4a4fd4_6 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: simint-0.7-h642920c_1 ...
installing: gau2grid-1.3.1-h035aef0_0 ...
installing: gmp-6.1.2-h6c8ec71_1 ...
installing: gsl-2.4-h14c3975_4 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: libxc-4.3.4-h7b6447c_0 ...
installing: metis-5.1.0-hf484d3e_4 ...
installing: mkl-2019.3-199 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1b-h7b6447c_1 ...
installing: tbb-2019.4-hfd86e86_0 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: glpk-4.65-h3ceedfd_2 ...
installing: hdf5-1.10.2-hba1933b_1 ...
installing: libedit-3.1.20181209-hc058e9b_0 ...
installing: libefp-1.5.0-h84097be_1 ...
installing: readline-7.0-h7b6447c_5 ...
installing: suitesparse-5.2.0-h9e4a6bb_0 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: ambit-0.3-h137fa24_1 ...
installing: chemps2-1.8.9-h8c3debe_0 ...
installing: sqlite-3.28.0-h7b6447c_0 ...
installing: asn1crypto-0.24.0-py36_0 ...
installing: atomicwrites-1.3.0-py36_1 ...
installing: attrs-19.1.0-py36_1 ...
installing: certifi-2019.3.9-py36_0 ...
installing: chardet-3.0.4-py36_1 ...
installing: cvxopt-1.2.0-py36hfa32c7d_0 ...
installing: dataclasses-0.6-py_0 ...
installing: decorator-4.4.0-py36_1 ...
installing: future-0.17.1-py36_0 ...
installing: idna-2.8-py36_0 ...
installing: jsonpickle-0.9.6-py36_0 ...
installing: more-itertools-7.0.0-py36_0 ...
installing: numpy-base-1.16.3-py36hde5b4d6_0 ...
installing: pcmsolver-1.2.1-py36h8733eb9_0 ...
installing: pluggy-0.11.0-py_0 ...
installing: py-1.8.0-py36_0 ...
installing: pycosat-0.6.3-py36h14c3975_0 ...
installing: pycparser-2.19-py36_0 ...
installing: pylibefp-0.4+f42ffb8-py36h5a86982_1 ...
installing: pysocks-1.7.0-py36_0 ...
installing: ruamel_yaml-0.15.46-py36h14c3975_0 ...
installing: six-1.12.0-py36_0 ...
installing: v2rdm_casscf-0.8-py36hc3560e4_6 ...
installing: wcwidth-0.1.7-py36_0 ...
installing: cffi-1.12.3-py36h2e261b9_0 ...
installing: deepdiff-3.3.0-py36_1 ...
installing: mkl_random-1.0.2-py36hd81dba3_0 ...
installing: pydantic-0.23-py36_0 ...
installing: setuptools-41.0.1-py36_0 ...
installing: cryptography-2.6.1-py36h1ba5d50_0 ...
installing: networkx-2.3-py_0 ...
installing: pint-0.9-py36_2 ...
installing: pytest-4.5.0-py36_0 ...
installing: wheel-0.33.4-py36_0 ...
installing: pip-19.1.1-py36_0 ...
installing: pyopenssl-19.0.0-py36_0 ...
installing: urllib3-1.24.2-py36_0 ...
installing: requests-2.21.0-py36_0 ...
installing: conda-4.6.14-py36_0 ...
installing: h5py-2.8.0-py36h989c5e5_3 ...
installing: mkl_fft-1.0.12-py36ha843d7b_0 ...
installing: numpy-1.16.3-py36h7e9f1db_0 ...
installing: qcelemental-0.4.0-py_0 ...
installing: resp-0.7-py36ha93d1a2_0 ...
installing: scipy-1.2.1-py36h7c811a0_0 ...
installing: openfermion-0.9-py36hd763080_1 ...
installing: psi4-1.3.2+ecbda83-py36h189457c_0 ...

  Thank you for installing Psi4.
    Website: psicode.org
    Forum:   forum.psicode.org
    Manual:  psicode.org/psi4manual/master/index.html
    GitHub:  github.com/psi4/psi4
    Binary:  anaconda.org/psi4/psi4
    Inputs:  /home/chenh/ly/sourcefolders/psi4conda/share/psi4/samples
    Test (after first activating conda installation or environment):
      psi4 /home/chenh/ly/sourcefolders/psi4conda/share/psi4/samples/sapt1/test.in
      psi4 --test

  For csh/tcsh command-line use, add to shell or ~/.tcshrc file:
    source /home/chenh/ly/sourcefolders/psi4conda/etc/profile.d/conda.csh
    conda activate
    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:
    source /home/chenh/ly/sourcefolders/psi4conda/etc/profile.d/conda.sh
    conda activate
    export PSI_SCRATCH=/path/to/existing/writable/local-not-network/disk/for/scratch/files

installing: snsmp2-1.0.3-py36he403277_2 ...
installing: openfermionpsi4-0.4-py36h934b37d_0 ...
installing: psi4-rt-1.3.2-py36ha6b60c8_0 ...
if: Expression Syntax.
ERROR: executing post_install.sh failed

$ cd /home/chenh/ly/sourcefolders/psi4conda/bin
$ ./psiv -V

Segmentation fault (core dumped)