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[VENETO] boboviz
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Message 49374 - Posted: 30 Apr 2018 | 9:45:46 UTC

I try to use Ubuntu 18.04, but i have all errors:

CondaValueError: prefix already exists: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml

Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/../../../libsimint.so: cannot read file data
During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/../../../libsimint.so: cannot read file data
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml
11:12:01 (1425): $PROJECT_DIR/miniconda/bin/python exited; CPU time 8.088141
11:12:01 (1425): app exit status: 0x1
11:12:01 (1425): called boinc_finish(195)

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Message 49377 - Posted: 30 Apr 2018 | 20:11:47 UTC - in response to Message 49374.
Last modified: 30 Apr 2018 | 20:30:44 UTC

I just ran one as a test with no problems.
http://www.gpugrid.net/results.php?hostid=475515
http://www.gpugrid.net/workunit.php?wuid=13460641

This is a new install of Ubuntu 18.04 on new hardware. If you upgraded, may a clean install would work?

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Message 49391 - Posted: 3 May 2018 | 14:29:50 UTC - in response to Message 49377.

I'll retry with a fresh installation...

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Message 49441 - Posted: 10 May 2018 | 19:25:12 UTC - in response to Message 49374.
Last modified: 10 May 2018 | 19:32:14 UTC

I just got one myself on Ubuntu 16.04. Maybe it was a recent update that did it? It will take someone with Linux expertise to figure it out.

But all the others are erroring after 35 seconds too.
http://www.gpugrid.net/results.php?hostid=448995&offset=0&show_names=0&state=5&appid=
Maybe something in the work unit changed. I have been off of QC for a few days, and it was working before.

<core_client_version>7.8.3</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
14:55:57 (29620): wrapper (7.7.26016): starting
14:55:57 (29620): wrapper (7.7.26016): starting
14:55:57 (29620): wrapper: running ../../projects/www.gpugrid.net/Miniconda3-4.3.30-Linux-x86_64.sh (-b -u -p /var/lib/boinc-client/projects/www.gpugrid.net/miniconda)
Python 3.6.3 :: Anaconda, Inc.
14:56:10 (29620): miniconda-installer exited; CPU time 11.388000
14:56:10 (29620): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)
Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml
15:00:31 (29620): $PROJECT_DIR/miniconda/bin/python exited; CPU time 141.956000
15:00:31 (29620): app exit status: 0x1
15:00:31 (29620): called boinc_finish(195)

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Message 49453 - Posted: 11 May 2018 | 13:28:23 UTC - in response to Message 49374.

I try to use Ubuntu 18.04, but i have all errors:


I am running 17.10 and am getting upgrade requests for 18 but have not jumped to it.

I have an RX570 using AMD PRO-17.50-511655 and I cannot use a "blank" screen saver or turn off the monitor as the gnome desktop locks up after a while. This seems to be a known Bug #1729028 but that bug was closed as no one has been complaining about it recently.

If 18.04 fixes this problem I may upgrade but I hate to mess with a working Linux box.

Are you using gnome desktop? If so, can you laave the system running overnight with the monitor turned off?

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Message 49475 - Posted: 14 May 2018 | 19:34:11 UTC
Last modified: 14 May 2018 | 19:35:56 UTC

They are still failing for me. Is anyone looking into this?
http://www.gpugrid.net/results.php?hostid=475515&offset=0&show_names=0&state=0&appid=30

NOTE: I use an app_config to allow only one work unit to run at a time (on 4 cores), so it is not the "startup problem".

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Message 49478 - Posted: 15 May 2018 | 6:39:38 UTC
Last modified: 15 May 2018 | 6:39:58 UTC

I tried a fresh installation of Ubuntu 17.10 and ALL my wu crashed after 5/10 minutes with the same error:

<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
22:11:21 (1668): wrapper (7.7.26016): starting
22:11:21 (1668): wrapper (7.7.26016): starting
22:11:21 (1668): wrapper: running ../../projects/www.gpugrid.net/Miniconda3-4.3.30-Linux-x86_64.sh (-b -u -p /var/lib/boinc-client/projects/www.gpugrid.net/miniconda)
Python 3.6.3 :: Anaconda, Inc.
22:11:37 (1668): miniconda-installer exited; CPU time 10.718316
22:11:37 (1668): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)

CondaValueError: prefix already exists: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml

ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'psi4::gcc-5-5.2.0-1'.
LinkError: post-link script failed for package psi4::gcc-5-5.2.0-1
running your command again with `-v` will provide additional information
location of failed script: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/bin/.gcc-5-post-link.sh
==> script messages <==
<None>

Attempting to roll back.

LinkError: post-link script failed for package psi4::gcc-5-5.2.0-1


It's a pity, please fix it

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Message 49479 - Posted: 15 May 2018 | 6:41:06 UTC - in response to Message 49453.

Are you using gnome desktop? If so, can you laave the system running overnight with the monitor turned off?


I use Lubuntu

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Message 49484 - Posted: 15 May 2018 | 16:15:03 UTC - in response to Message 49478.

I tried a fresh installation of Ubuntu 17.10 and ALL my wu crashed after 5/10 minutes with the same error


Today, with fresh installation of Lubuntu 14.04 with no updates (and an older version of Boinc). Same errors.

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Message 49485 - Posted: 15 May 2018 | 16:22:21 UTC - in response to Message 49484.

Today, with fresh installation of Lubuntu 14.04 with no updates (and an older version of Boinc). Same errors.

I think that proves it is a problem with the application (or data). I had thought it might be due to a recent security update for Ubuntu 16.04, which would place it on the same level as Ubuntu 18.04. But that is not the case. Thanks for checking.

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Message 49487 - Posted: 16 May 2018 | 3:02:08 UTC

Here are some more clues. I have an install from on or about April 28, 2018 that works fine. Starting on or about April 30, many new installs seem to fail. I tried a new install on May 5 that failed.

In looking at run logs, a successful task runs for about 30 seconds, downloads a small amount of data, gives this message:

CondaValueError: prefix already exists: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml

then starts running on all 4 "CPU's" to a normal completion.

An unsuccessful task starts up, downloads data for about 5 minutes, then gives the following error messages and aborts.

09:59:20 (1889): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)
ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'psi4::gcc-5-5.2.0-1'.
LinkError: post-link script failed for package psi4::gcc-5-5.2.0-1
running your command again with `-v` will provide additional information
location of failed script: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/bin/.gcc-5-post-link.sh
==> script messages <==
<None>

Attempting to roll back.

LinkError: post-link script failed for package psi4::gcc-5-5.2.0-1
running your command again with `-v` will provide additional information
location of failed script: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/bin/.gcc-5-post-link.sh
==> script messages <==
<None>

Traceback (most recent call last):
File "pre_script.py", line 20, in <module>
raise Exception("Error installing psi4 dev")
Exception: Error installing psi4 dev



It appears that something happened to the job setup between April 28 and April 30 that causes a new install to have problems.

As a test, I copied the entire /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/ folder from the known good setup from April 28 to the new setup that I was working on today. With that in place, the new install completed a QC tasks normally and has started another one.

Computer ID for the new setup is 476647 if you want to take a look. My Linux skills are limited so it took me a while to get the right combination of copy, paste, folder location and security permissions. If you look at tasks processed, you will see several errors until I stumbled onto the magic solution.

Please let me know if you have questions or need more information.

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Message 49488 - Posted: 16 May 2018 | 10:50:44 UTC - in response to Message 49487.

Can you check if you have the gcc package installed? AFAIK it is not by default.

Thanks

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Message 49489 - Posted: 16 May 2018 | 12:36:21 UTC

Toni,

gcc was not installed when I ran the first test. I installed it then started getting different error messages until I copied the miniconda folder.

Hope that helps.

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Message 49490 - Posted: 16 May 2018 | 12:36:47 UTC - in response to Message 49488.

Can you check if you have the gcc package installed?


I update the gcc on old lubuntu to 4.8.4 version.
Errors continue:
14:33:26 (3195): miniconda-installer exited; CPU time 11.220000
14:33:26 (3195): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)

CondaValueError: prefix already exists: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml

Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml

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Message 49491 - Posted: 16 May 2018 | 13:33:52 UTC - in response to Message 49488.

I tried it on a different machine, a Ryzen 1700 with Lubuntu 17.10.1.

First I checked the gcc: "gcc is already the newest version (4:7.2.0-1ubuntu1)"
Then I updated everything, and am now running Linux 4.13.0-41
Finally, I downloaded a single QC work unit (4 cores). It ran for three minutes.

<core_client_version>7.8.3</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
09:23:38 (8952): wrapper (7.7.26016): starting
09:23:38 (8952): wrapper (7.7.26016): starting
09:23:38 (8952): wrapper: running ../../projects/www.gpugrid.net/Miniconda3-4.3.30-Linux-x86_64.sh (-b -u -p /var/lib/boinc-client/projects/www.gpugrid.net/miniconda)
Python 3.6.3 :: Anaconda, Inc.
09:23:47 (8952): miniconda-installer exited; CPU time 7.696161
09:23:47 (8952): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)
Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml
09:26:42 (8952): $PROJECT_DIR/miniconda/bin/python exited; CPU time 101.619166
09:26:42 (8952): app exit status: 0x1
09:26:42 (8952): called boinc_finish(195)

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Message 49497 - Posted: 17 May 2018 | 21:46:27 UTC

Problems with all -buntu distro. I'll try a Fedora...

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Message 49500 - Posted: 18 May 2018 | 4:02:21 UTC

As I wrote in News all CPU tasks on my SuSE Leap 42.3 Linux fail miserably. GPU tasks on the same computer, a SUN Workstation with Opteron 1210 and a GTX 750 Ti board complete and validate.
Tullio

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Message 49505 - Posted: 19 May 2018 | 8:06:02 UTC

I'm getting the same error on Arch Linux.

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Message 49507 - Posted: 19 May 2018 | 8:49:30 UTC

I should need an explanation. When I have a Linux task waiting to start and I click on its Properties I see an executable called wrapper that is very similar to the vboxwrapper of LHC@home tasks. But when it starts and goes on for about 5 minutes the Linux (and UNIX) "top" command show a "python" running. Which is the relationship between the two executables?
Tullio

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Message 49520 - Posted: 22 May 2018 | 13:53:32 UTC - in response to Message 49519.
Last modified: 22 May 2018 | 14:40:38 UTC

Surely the major distributions should work as long as you have gcc installed.

Something to try is to reset the project. This should delete the (large-ish) miniconda executable and download it again at the next start (which takes a couple of minutes). Beware, reset stop GPU WUs too!

Reset is likely necessary if you upgrade the OS.

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Message 49522 - Posted: 22 May 2018 | 14:23:17 UTC - in response to Message 49500.
Last modified: 22 May 2018 | 14:41:27 UTC

@tullio: vboxwrapper calls the actual application(s). In our case: python, a language interpreter. It's normal behaviour.

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Message 49523 - Posted: 22 May 2018 | 16:57:22 UTC - in response to Message 49520.

Surely the major distributions should work as long as you have gcc installed.

gcc --version
gcc (Ubuntu 7.3.0-16ubuntu3) 7.3.0


Something to try is to reset the project. This should delete the (large-ish) miniconda executable and download it again at the next start (which takes a couple of minutes). Beware, reset stop GPU WUs too!

This is a new install of Ubuntu 18.04, not an upgrade, and I have reset it several times.
http://www.gpugrid.net/results.php?hostid=475515&offset=0&show_names=0&state=5&appid=30

I think the previous posts show when the problem started.

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Message 49525 - Posted: 22 May 2018 | 17:51:43 UTC

Could this be a python problem that myself and others observed with new installs of linux mint 18.3?

This solved the QC error problem for us:

wget http://launchpadlibrarian.net/109052632/python-support_1.0.15_all.deb

sudo dpkg -i python-support_1.0.15_all.deb

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Message 49526 - Posted: 22 May 2018 | 18:32:51 UTC - in response to Message 49525.

It looks very promising, but I have reached my daily limit due to the errors. Maybe someone else can try it?

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Message 49527 - Posted: 22 May 2018 | 20:50:21 UTC

There is a similar python version issue with the FAHControl app over at Folding@home. Apparently Ubuntu 18.04 has python 3 installed so you may have to install python 2. Here is the link over at the folding forum

https://foldingforum.org/viewtopic.php?f=96&t=30778


For the QC app I've found:

linux mint 17.3, the python version is 2.7.6 and it works fine.

Linux mint 18.3, the python version is 2.7.12 and the QC app errors out.

As posted above installing the python-support_1.0.15_all.deb package solves the problem

wget http://launchpadlibrarian.net/109052632/python-support_1.0.15_all.deb

sudo dpkg -i python-support_1.0.15_all.deb

You can check the python version with:

python --version
or
python -V

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Message 49529 - Posted: 23 May 2018 | 1:12:00 UTC

On my SuSE Leap 42.3 Linux python is 2.7.13. Is this the problem? By the way, I have followed an online course on python via edx/Berkeley and I don't like it. They made use of Jupyter Notebooks which is an Interactive python developed at UC Berkeley campus, whose authors received a prize by the Association for Computing Machinery,as reported in the Berkeley Online Newsletter which I receive. But why use an interpreter? CERN uses Scientific Linux which is RedHat plus some CERN libraries, and VirtualBox in its LHC@home projects, which I run on Windows 10 and SuSE Linux. I would gladly help GPUGRID CPU tasks but they all fail.
Tullio

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Message 49532 - Posted: 23 May 2018 | 8:57:14 UTC

@Tullio, Is there a way on openSuse to "force" the QC app to use python 2.6?

At the folding forum, there are instructions for openSuse users to set up fahcontrol to use python 2.6 vs 2.7.

See step 2 at this link.

https://foldingforum.org/viewtopic.php?f=89&t=30335

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Message 49533 - Posted: 23 May 2018 | 9:53:18 UTC

@Tullio, It looks like the QC app looks for python 3.6.3. I'm not sure what you need to get it working on openSuse. Sorry.

Perhaps the developers could release a version of the QC app for python 2.7?

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Message 49537 - Posted: 23 May 2018 | 14:50:51 UTC - in response to Message 49525.

This solved the QC error problem for us:
wget http://launchpadlibrarian.net/109052632/python-support_1.0.15_all.deb
sudo dpkg -i python-support_1.0.15_all.deb

Unfortunately, I am still getting the python error.

<core_client_version>7.9.3</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
08:41:20 (3377): wrapper (7.7.26016): starting
08:41:20 (3377): wrapper (7.7.26016): starting
08:41:20 (3377): wrapper: running ../../projects/www.gpugrid.net/Miniconda3-4.3.30-Linux-x86_64.sh (-b -u -p /var/lib/boinc-client/projects/www.gpugrid.net/miniconda)
Python 3.6.3 :: Anaconda, Inc.
08:41:29 (3377): miniconda-installer exited; CPU time 7.627092
08:41:29 (3377): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)

CondaValueError: prefix already exists: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml

Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml
08:41:39 (3377): $PROJECT_DIR/miniconda/bin/python exited; CPU time 8.040848
08:41:39 (3377): app exit status: 0x1
08:41:39 (3377): called boinc_finish(195)


I also installed Folding 7.5.0 (before installing the above python), but did not have any python problems there. Something strange is going on, but thanks for your help.

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Message 49538 - Posted: 23 May 2018 | 14:56:59 UTC - in response to Message 49537.
Last modified: 23 May 2018 | 14:57:57 UTC

In Jim's case the key is this:

... __svml_sin4


This may be a different failure from other people's.

There is something odd in the acceleration libraries, as if they are not found. Not easy to debug. I guess you already tried the reset, right?

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Message 49539 - Posted: 23 May 2018 | 15:15:00 UTC - in response to Message 49538.
Last modified: 23 May 2018 | 15:28:33 UTC

I guess you already tried the reset, right?

Yes, several times. And it should be a standard installation of Ubuntu 18.04, though I was getting it earlier on my Ubuntu 16.04 machine as well.

EDIT: Just to check, I reattached my Ubuntu 16.04 machine (i7-3770), and downloaded only a single work unit (running on 4 cores). But I still got a python error. Whether it is the same one as on the 18.04 machine I don't know.

<core_client_version>7.8.3</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
11:19:58 (19485): wrapper (7.7.26016): starting
11:19:58 (19485): wrapper (7.7.26016): starting
11:19:58 (19485): wrapper: running ../../projects/www.gpugrid.net/Miniconda3-4.3.30-Linux-x86_64.sh (-b -u -p /var/lib/boinc-client/projects/www.gpugrid.net/miniconda)
Python 3.6.3 :: Anaconda, Inc.
11:20:05 (19485): miniconda-installer exited; CPU time 6.042732
11:20:05 (19485): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)
Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml
11:23:12 (19485): $PROJECT_DIR/miniconda/bin/python exited; CPU time 76.348243
11:23:12 (19485): app exit status: 0x1
11:23:12 (19485): called boinc_finish(195)

http://www.gpugrid.net/result.php?resultid=17462427

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Message 49540 - Posted: 23 May 2018 | 15:32:32 UTC - in response to Message 49539.

Thanks, looks like the same error. Will need to debug it locally.

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Message 49541 - Posted: 23 May 2018 | 15:39:50 UTC - in response to Message 49540.

I think on some projects (maybe Rosetta or Folding, I don't recall) they are talking about recent changes concerning static versus dynamic linking of Linux/Ubuntu libraries that are causing problems, but I know nothing about that. Good luck.

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Message 49542 - Posted: 23 May 2018 | 16:20:02 UTC

When I update the kernel modules of VirtualBox after a kernel upgrade on my SuSE Learn 42.3, the installer says it found Python and proceeds.I must confess I don't know much about Python despite taking a course and I would not like to download a version that the VirtualBox installer cannot use.Since VirtualBox is vital for me to run the CERN projects of LHC@home, I am not fiddling with it. Sorry.
Tullio

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Message 49543 - Posted: 23 May 2018 | 17:41:56 UTC

There has been a recent discussion of the differences and incompatibilities between Python 2 and Python 3 on BOINC's GitHub page - primarily directed at Python as used on the server, but it may be helpful here.

Port to Python3 #2475

Keep reading through (it's a long thread): there are some pointers to useful tools like 2to3 and python-future towards the end.

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Message 49544 - Posted: 23 May 2018 | 18:35:18 UTC - in response to Message 49543.
Last modified: 23 May 2018 | 18:42:03 UTC

The only time when GpuGrid scientists will condescend to involve themselves in dialogue with you is when they have something they want so enjoy the experience.
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Message 49548 - Posted: 23 May 2018 | 20:37:02 UTC

__svml_sin4


I have an older install on disk so I could take a look. The old install worked so lets first check where the symbol was defined.

$ cd boinc/projects/www.gpugrid.net/miniconda/envs/qmml/ $ grep -r svml_sin4 lib/ Binary file lib/libgdma.so matches Binary file lib/python3.6/site-packages/psi4/core.so matches


A quick peek to core.so to verify the search result.

$ objdump -t lib/python3.6/site-packages/psi4/core.so | grep svml_sin4 0000000000000000 F *UND* 0000000000000000 __svml_sin4


Undefined there as it should be. Next libgdma.so.

$ objdump -t lib/libgdma.so | grep svml_sin4 00000000004140e0 l O .data 0000000000000008 __svml_sin4_chosen_core_func 000000000040a4c0 l O .data.rel.ro 0000000000000060 __svml_sin4_dispatch_table 0000000000185c90 g F .text 00000000000008b0 __svml_sin4_e9 0000000000186540 g F .text 00000000000005f0 __svml_sin4_l9 00000000001849e0 g F .text 0000000000000010 __svml_sin4 0000000000184a00 g F .text 0000000000000130 __svml_sin4_chosen_core_func_init 00000000001849f0 g F .text 0000000000000010 __svml_sin4_chosen_core_func_get_ptr


Ok. __svml_sin4 is a function and was defined in libgdma.so.

To see how things are now I made a new miniconda installation and made a new environment there according to the pre_script.py. Running Python manually and trying to import psi4 fails with the undefined symbol error. Lets see what's going on.

$ grep -r svml_sin4 lib/ Binary file lib/python3.6/site-packages/psi4/core.so matches $ objdump -t lib/python3.6/site-packages/psi4/core.so | grep svml_sin4 0000000000000000 F *UND* 0000000000000000 __svml_sin4


Ok. The symbol is still undefined in core.so but there is no lib where it is defined. Package lists tell what happened.

OLD NEW attrs 17.4.0 py36_0 18.1.0 py36_0 blas 1 mkl ca-certificates 2017.08.26 h1d4fec5_0 2018.03.07 0 certifi 2018.1.18 py36_0 2018.4.16 py36_0 chemps2 1.8.4 0 1.8.4 0 psi4/label/dev cloog 0.18.0 0 0.18.0 0 dftd3 3.2.0 7 3.2.0 h0e1e685_8 psi4/label/dev dkh 1.2 1 1.2 h173d85e_2 psi4/label/dev erd 3.0.6 1 3.0.6 1 psi4/label/dev gcc-5 5.2.0 1 5.2.0 1 psi4 gcc-5-mp 5.2.0 0 5.2.0 0 psi4 gdma 2.2.6 3 2.2.6 hf4d0741_5 psi4/label/dev gmp 6.1.2 h6c8ec71_1 6.1.2 h6c8ec71_1 h5py 2.7.0 np113py36_0 2.7.0 np113py36_0 hdf5 1.8.17 2 1.8.17 2 intel-openmp 2018.0.0 hc7b2577_8 2018.0.0 8 isl 0.12.2 0 0.12.2 0 libedit 3.1 heed3624_0 3.1.20170329 h6b74fdf_2 libefp 1.5b1 0 1.5.0 h66000e6_0 psi4/label/dev libffi 3.2.1 hd88cf55_4 3.2.1 hd88cf55_4 libgcc-ng 7.2.0 h7cc24e2_2 7.2.0 hdf63c60_3 libgfortran-ng 7.2.0 h9f7466a_2 7.2.0 hdf63c60_3 libint 1.2.1 1 1.2.1 h73b9bb0_3 psi4/label/dev libstdcxx-ng 7.2.0 h7a57d05_2 7.2.0 hdf63c60_3 libxc 3.0.0 6 3.0.0 6 psi4/label/dev mkl 2018.0.1 h19d6760_4 2018.0.2 1 mkl_fft 1.0.1 py36h3010b51_0 mkl_random 1.0.1 py36h629b387_0 more-itertools 4.1.0 py36_0 mpc 1.0.1 0 1.0.1 0 mpfr 3.1.2 0 3.1.2 0 ncurses 6 h9df7e31_2 6.1 hf484d3e_0 numpy 1.13.3 py36h3dfced4_2 1.13.3 py36hdbf6ddf_4 numpy-base 1.14.3 py36h9be14a7_1 openssl 1.0.2n hb7f436b_0 1.0.2o h20670df_0 pcmsolver 1.1.10 py36_1 1.1.10 py36_1 psi4/label/dev pip 9.0.1 py36h6c6f9ce_4 10.0.1 py36_0 pluggy 0.6.0 py36hb689045_0 0.6.0 py36hb689045_0 psi4 1.2a1.dev611+8fe3513 py36_0 1.2a1.dev611+8fe3513 py36_0 psi4/label/dev psi4-lt-mp 1.2a1.dev3 py36_0 1.2a1.dev3 py36_0 psi4/label/dev py 1.5.2 py36h29bf505_0 1.5.3 py36_0 pytest 3.3.2 py36_0 3.5.1 py36_0 python 3.6.4 hc3d631a_1 3.6.5 hc3d631a_2 readline 7 ha6073c6_4 7 ha6073c6_4 setuptools 38.4.0 py36_0 39.1.0 py36_0 simint 0.7 0 psi4 0.7 0 psi4 six 1.11.0 py36h372c433_1 1.11.0 py36h372c433_1 sqlite 3.22.0 h1bed415_0 3.23.1 he433501_0 tk 8.6.7 hc745277_3 8.6.7 hc745277_3 wheel 0.30.0 py36hfd4bba0_1 0.31.1 py36_0 xz 5.2.3 h55aa19d_2 5.2.4 h14c3975_4 zlib 1.2.11 ha838bed_2 1.2.11 ha838bed_2


So gdma package along with a several others have been updated and that broke the psi4 package that has not been updated.

The package can be downgraded with bin/conda install -n qmml -c psi4/label/dev -c psi4 gdma=2.2.6=3 and at least manually running Python and importing psi4 works again. I haven't tested actually running tasks yet.


@Toni

I would suggest that you pin not only Psi4 package version but also all of its main dependencies.

Also. While doing some research about this I came about some information that Psi4 switched from statically linked MKL to dynamically linked MKL because static linking resulted in weird issues such as bad math results. SVML is Intel's Short Vector Math Lib and I'm not entirely sure how it relates to MKL. But I hope you have done some pre-screening of the results you have gotten back so far and checked that they are good.

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Message 49549 - Posted: 24 May 2018 | 9:14:16 UTC - in response to Message 49527.
Last modified: 24 May 2018 | 9:15:37 UTC

Linux mint 18.3, the python version is 2.7.12 and the QC app errors out.

As posted above installing the python-support_1.0.15_all.deb package solves the problem

wget http://launchpadlibrarian.net/109052632/python-support_1.0.15_all.deb

sudo dpkg -i python-support_1.0.15_all.deb


No way.
- Fresh install of Mint 18.3
- Update install (sudo apt-get update/upgrade)
- wget http://launch....
- sudo dpkg -i python-support...
- gcc -v: gcc version 5.4.0 20160609
- python --version: python 2.7.12

Stops at 1,098% and after few minutes crashes:

ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'psi4::gcc-5-5.2.0-1'.
LinkError: post-link script failed for package psi4::gcc-5-5.2.0-1
running your command again with `-v` will provide additional information
location of failed script: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/bin/.gcc-5-post-link.sh
==> script messages <==
<None>

Attempting to roll back.

LinkError: post-link script failed for package psi4::gcc-5-5.2.0-1
running your command again with `-v` will provide additional information
location of failed script: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/bin/.gcc-5-post-link.sh
==> script messages <==
<None>

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Message 49550 - Posted: 24 May 2018 | 15:14:06 UTC - in response to Message 49548.

@Juha: thanks, sounds exactly that. I'll try to pin asap. Thanks a lot.

@everybody: this is ONLY related to the "undefined symbol" error. Other errors have other causes.

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Message 49551 - Posted: 24 May 2018 | 15:35:24 UTC - in response to Message 49549.

I installed build-essential which includes gcc on my mint 18.3 clean install.

sudo apt install build-essential

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Message 49552 - Posted: 24 May 2018 | 18:34:36 UTC - in response to Message 49551.
Last modified: 24 May 2018 | 18:34:53 UTC

I installed build-essential which includes gcc on my mint 18.3 clean install.

My version of build-essential on my Ubuntu 16.04 and 18.04 machines is the latest version (12.4ubuntu1), and it still does not work.

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Message 49560 - Posted: 28 May 2018 | 12:40:11 UTC - in response to Message 49552.

Thanks to Juha's debugging, we hopefully are about to fix the "svml_sin4" problem. We'll need to cancel the running workunits though.

t

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Message 49566 - Posted: 30 May 2018 | 13:13:24 UTC

@boboviz I had the same problem on a VM because it had gcc but was missing the C libraries. Try `sudo apt-get install gcc` which should install the libs as well.

As on the python2/3 subject, the system python should not matter for us. We use a conda environment where we install python3 which is what our programs need.

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Message 49567 - Posted: 30 May 2018 | 13:19:01 UTC

On the gdma issue. I just sent out a single workunit with fixed gmda version as a test. If it comes back fine I'll cancel all current WUs and send out new ones.

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Message 49568 - Posted: 30 May 2018 | 15:02:55 UTC

It's like a little nightmare.

- VirtualBox VM with Mint 17.3
- sudo apt-get update/upgrade
- sudo apt-get install gcc ("gcc is already the newest version")
- sudo apt-get install buid essential
- wget http://launchpadlibrarian.net/109052632/python-support_1.0.15_all.deb
- sudo dpkg -i python-support_1.0.15_all.deb
- sudo apt-get install boinc-client boinc-manager (7.2.42)
- gcc -v = 4.8.4
- python --version: 2.7.6

And...svml_sin4!!


16:46:38 (2487): wrapper: running /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/bin/python (pre_script.py)
Traceback (most recent call last):
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 55, in <module>
from . import core
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run-qmml.py", line 12, in <module>
import psi4
File "/var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/__init__.py", line 60, in <module>
raise ImportError("{0}".format(err))
ImportError: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml/lib/python3.6/site-packages/psi4/core.so: undefined symbol: __svml_sin4
Traceback (most recent call last):
File "pre_script.py", line 31, in <module>
raise Exception("Error running qmml")
Exception: Error running qmml
16:51:34 (2487): $PROJECT_DIR/miniconda/bin/python exited; CPU time 132.140000
16:51:34 (2487): app exit status: 0x1
16:51:34 (2487): called boinc_finish(195)


I think i'll wait the Windows version....

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Message 49569 - Posted: 31 May 2018 | 8:56:59 UTC
Last modified: 31 May 2018 | 8:57:16 UTC

Hm sorry I can't help you with this error then :( We are working on the Windows version though so hopefully in a month or two (or three)...

So I fixed the gdma version and my first WU went through and computed fine. Can't guarantee that this will fix the problem on all machines as it seemed like the machine that computed my WU already had a working conda install but I'll go ahead and send out more of my WUs and see what happens.

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Message 49570 - Posted: 31 May 2018 | 11:39:29 UTC

I cancelled the remaining old WUs and sent out 250 of my new ones. Let's see if it solves the issues. If everything goes fine I will submit many more.

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Message 49571 - Posted: 31 May 2018 | 14:27:53 UTC

Okay so the error % is at 10% currently with 120 jobs completed and 13 failed.
The ones that failed, did so on users which already had completed lots more jobs so I'll scratch it up to chance or single bad host of those users as the errors are not consistent.

I am currently uploading thousands of jobs. Happy crunching :)

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Message 49572 - Posted: 31 May 2018 | 16:07:37 UTC - in response to Message 49571.

I am currently uploading thousands of jobs. Happy crunching :)


I'll try this new version.

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Message 49573 - Posted: 31 May 2018 | 16:09:16 UTC - in response to Message 49572.

Give it a try, although I doubt it will solve the gcc problem you have (but one can always hope)

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Message 49574 - Posted: 31 May 2018 | 16:26:44 UTC - in response to Message 49573.

Give it a try, although I doubt it will solve the gcc problem you have (but one can always hope)



It runs!! It runs!!
Only a little error (CondaValueError: prefix already exists: /var/lib/boinc-client/projects/www.gpugrid.net/miniconda/envs/qmml), but "completed and validated"

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Message 49575 - Posted: 31 May 2018 | 17:43:48 UTC

I've finished 34 of the new Work Units and all are valid.

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Message 49576 - Posted: 31 May 2018 | 21:53:54 UTC

@boboviz as far as I can tell this error is ignored.
Happy to hear that it's running again though :)

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Message 49685 - Posted: 17 Jun 2018 | 15:56:57 UTC

CPU tasks seem to run well on my HP Laptop with SuSE Linux Leap 42.3. Thy used to fail.
Tullio

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