Psi4conda Installer Problem on Mac

build
1

Hi,

Following the steps in Psi4conda installer I was able to install psiconda with this problem while running the script:

dyld: lazy symbol binding failed: Symbol not found: dpotrf
Referenced from: /Users/bykov/psi4conda/bin/psi4
Expected in: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

Tests in the end of the installation passed, but when I then try to run the test:

psi4 “$(dirname $(which psi4))”/…/share/psi4/samples/sapt1/test.in

I am getting the same error from above:

dyld: Symbol not found: dpotrf
Referenced from: /Users/bykov/miniconda/bin/psi4
Expected in: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

Abort trap: 6

It seems that linking to Lapack doesn’t work properly on my mac (recently updated to sierra). Some googling the problem suggests that some libraries in mac os x sierra have been updated and obviously some lapack function names have been changed resulting in the problem.

So, could someone from the developers update the script? Or maybe there is a way to tell the script to use different Lapack installed on my mac?

I would appreciate any help!

Thanks!

All the best,
Dima

2

Hmm, it should be in libLAPACK.dylib. Can you run:
nm /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib | grep dpotrf

and post the output here.

3

Grepping through the libLAPACK.dylib gives:

nm /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib | grep dpotrf
00000000000039e6 T _dpotrf
00000000000039e6 T dpotrf
000000000000352b t _dpotrf_Column_Lower
000000000000302d t _dpotrf_Column_Upper

So, obviously the function is in libLAPACK, but in my error message Psi4 expecting “dpotrf” to be in libBLAS and it is not there. I also read on web that mac was changing libraries to avoid duplications. So, maybe this function used to be in both, but not any more.

4

The psi4conda is 1.0. Would you want to give pre-1.1 a try? Besides the code, main differences are it’s built on computer with newer OS and it’s clang/libc++ based not gcc/libstdc++ based, so only blas/lapack parallelism.

It’s not packaged up with Mini/Anaconda, but once you have one of those installed (directions), just conda create -n p4py35 python=3.5 psi4 numpy dftd3 -c psi4/label/clang -c psi4 (or 2.7 if you’d rather). You want a version with “1.1a2” in it.

5

The pre-1.1 works out of the box. Everything is fine with the tests. Thanks for the help!

6

I had a similar problem to bykov reported above. I ran the installation as suggested by lorlab and it finished with a not to

To activate this environment, use:

> source activate p4py35

without running that, my system would respond with “-bash: ps4: command not found” following my typing psi4, even if I set the directory equal to the one with psi4 inside. After executing the “source activate p4py35” command, when I now enter psi4 I get response:

Traceback (most recent call last):
File “/Users/Kevin_old/miniconda3/envs/p4py35/bin/psi4”, line 210, in
exec(content)
File “”, line 20

^
SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/Kevin_old/miniconda3/envs/p4py35/bin/psi4”, line 219, in
tb_str += error_msg.message
AttributeError: ‘SyntaxError’ object has no attribute ‘message’

Anyone have a suggestion for how for fix this problem?

7

Have you tried running one of the test.in files in samples?