virtual memory exhausted: Cannot allocate memory

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Austin

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Mar 12, 2019, 12:54:06 PM3/12/19

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Hi,

After reinstalling and recompiling for the new updates. In running make for the atomspace. I get errors such as virtual memory exhausted: Cannot allocate memory.Find attached the error images in detail.

Please what could cause this; The AWS EC2 instance type used is t3.large. Also, I am wondering if any specific recommendations of memory size required to run all of opencog efficiently ?

Greatly appreciate any help provided.

Thank you!

Screenshot 2019-03-12 at 16.14.59.png

Vitaly Bogdanov

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Mar 13, 2019, 12:06:25 PM3/13/19

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Hi Austin,

My machine has 16 Gib of RAM, 5 of them are occupied by operating system almost constantly. At least it is enough to build opencog. I have just make a test and I didn't see more than 2 GiB were used during build. Have you tried executing "free" command to see how much of free memory do you have?

Best regards,

Vitaly

Nil Geisweiller

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Mar 14, 2019, 2:21:07 AM3/14/19

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Hi Austin,

opencog (with the exception of MOSES that takes a crazy 4GB due to
template overuse) can be compiled on a RPi 2 (1GB of RAM), so it's weird
that it doesn't compile on your instance. I can recall AWS EC2 being
prone to memory issues due to disabled swap, but never during compiling.

Maybe look into using ulimit or gcc -ftime-report as suggested here
https://stackoverflow.com/questions/12964013/reducing-memory-allocation-gcc-command#12964053

Nil

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Austin

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Mar 15, 2019, 6:39:12 AM3/15/19

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Hi Vitaly

Thank you for your reply! Yes indeed, I do have enough free memory. I have been able to build the atomspace by running make -j4.

I understand without the number, it spawns a process for each core I have; so it builds with only test 16 - ParallelUTest failing (SEGFAULT).

However, I'll try the docker image if it makes things easier for regular updating and rebuilding of the libraries. Thanks again!

Best,

Austin

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Screenshot 2019-03-15 at 09.53.23.png

Austin

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Mar 15, 2019, 6:47:10 AM3/15/19

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Hi Nil,

Thank you so much for that piece of information. Yes, Indeed! the machine seems to prefer that I specify the memory resources allocated.

Best,

Austin

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Vitaly Bogdanov

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Mar 15, 2019, 8:32:04 AM3/15/19

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ParallelUTest issue should be fixed in latest master, please see https://github.com/opencog/atomspace/issues/2127

Austin

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Mar 19, 2019, 6:52:49 AM3/19/19

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Hello people!

Hope you are doing well. Since the last update, With cogutil and Atomspace building fine. some of the make tests for the opencog directory have failed on my end. Even though it seems to make ok. Please find attached a screenshot of these errors.

Also for a better work process; I'm trying to figure out how to work with docker. I would like to use opencog's atomspace in production through docker. However in building opencog with "docker-compose run --service-ports dev". There seems to be no module called "opencog.atomspace" in this dev docker container. Does atomspace exist as a different container ? If not, what changes may need to be made to make use of atomspace in the opencog docker environment ?

Thank you in advance :)

Austin

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Screenshot 2019-03-19 at 10.36.29.png

Nil Geisweiller

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Mar 19, 2019, 7:49:02 AM3/19/19

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Hi Austin,

you might need to install opencog before running the unit tests.

Nil

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Austin

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Mar 19, 2019, 2:04:04 PM3/19/19

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Thanks Nil,

After reinstalling and doing that, now 3 of the tests still continue to fail.

Austin

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Screenshot 2019-03-19 at 16.11.49.png

Nil Geisweiller

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Mar 19, 2019, 2:14:31 PM3/19/19

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On 3/19/19 8:03 PM, Austin wrote:
> After reinstalling and doing that, now 3 of the tests still continue to
> fail.

They also fail for me.

Nil

> > <mailto:vsb...@gmail.com <mailto:vsb...@gmail.com>>> wrote:
> >
> > ParallelUTest issue should be fixed in latest master, please see
> > https://github.com/opencog/atomspace/issues/2127
> >
> > On Friday, March 15, 2019 at 1:39:12 PM UTC+3, Austin wrote:
> >
> > Hi Vitaly
> >
> > Thank you for your reply! Yes indeed, I do have enough free
> > memory. I have been able to build the atomspace by
> running make -j4.
> > I understand without the number, it spawns a process for each
> > core I have; so it builds with only test 16 - ParallelUTest
> > failing (SEGFAULT).
> > However, I'll try the docker image if it makes
> things easier for
> > regular updating and rebuilding of the libraries. Thanks
> again!
> >
> > Best,
> > Austin
> >
> >
> >
> > On Wed, Mar 13, 2019 at 4:06 PM Vitaly Bogdanov

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Linas Vepstas

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Mar 19, 2019, 2:21:01 PM3/19/19

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Hmm. ShellUTest should pass -- There are two incompatible versions of netcat, and ShellUTest assumes one of them. That should be fixed. Anaphora should pass, although sometimes python gets in the way. AtomSpacePublisher is just unmaintained and obsolete. --linas

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Johannes Castner

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Mar 20, 2019, 6:48:18 AM3/20/19

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Hi Nil and Linas,

Austin and I are working together and our biggest problem isn't that those three tests fail, but rather that we cannot import certain things and perhaps they're missing (?):

Traceback (most recent call last):
File "scheme_router.py", line 5, in <module>
from opencog.atomspace import types
ImportError: libattentionbank.so: cannot open shared object file: No such file or directory

We thought that the same problem that makes these tests fail might also be responsible for the above error? We're desperately trying to figure out how we can better build the system in a reliable way, such that once we run into a bug and lets say, you've fixed that bug in your code, we can quickly update from your code and then set everything up again and have a working system. Right now, every time we update it is exceedingly hard to get back to where we were before, minus the bug that made us want to reset in the first place. Is there some way you could maybe guide us to how we can have a system that follows all of your improvements and bug fixes and that doesn't have problems with setting up and installing? I would love us to be able to contribute more and spend less time setting up the three libraries again and again. If it were easy to set them all up--i.e. if there were a script that reliably sets them up and tests them, this would improve things massively!

With gratitude and great appreciation,

Johannes

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Nil Geisweiller

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Mar 20, 2019, 8:11:56 AM3/20/19

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Hi,

sorry to hear about that.

I have the following scripts in my opencog repos.

To purge opencog from my system:

==== clean-opencog.sh ====
sudo rm -fr /usr/local/include/opencog
sudo rm -fr /usr/local/share/opencog
sudo rm -fr /usr/local/lib/opencog
sudo rm -fr /usr/share/guile/site/2.2/opencog*
sudo rm -fr /usr/local/share/guile/site/2.2/opencog*
rm -fr ~/.cache/guile
==========================

To build opencog

==== build.sh ====
rm -fr build
mkdir build
cd build
cmake ..
make -j4 && sudo make install
cd ..
===================

When I get weird errors, I run clean-opencog.sh, then rebuild cogutil,
atomspace, opencog (and possibly more) with my build scripts.

I very have rarely problems and since I use ccache (with an SSD) it is
usually very fast.

Now my clean script doesn't purge python modules because I do not use
Python, but that should be easy to add.

Hopefully it helps, let us know otherwise.

Nil

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Johannes Castner

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Mar 20, 2019, 10:56:21 AM3/20/19

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Hi Nil,

Thank you for answering so quickly! Awesome, we’ll try your scripts and hopefully it’ll run! Could you tell us a bit more about the ccache you’re doing? I know absolutely nothing about these things and all hints help tremendously!

Thank you!

Johannes

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Nil Geisweiller

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Mar 20, 2019, 12:32:54 PM3/20/19

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Hi Johannes,

On 3/20/19 4:56 PM, Johannes Castner wrote:
> hopefully it’ll run! Could you tell us a bit more about the ccache
> you’re doing? I know absolutely nothing about these things and all
> hints help tremendously!

Assuming you wish to use ccache all the time (which I recommend if you
have a fast HDD, or better an SSD), just create symbolic links to gcc.

So after installing ccache (assuming you're using a Debian-based OS like
Ubuntu)

sudo apt-get install ccache

type the following

sudo cp /usr/bin/ccache /usr/local/bin/ccache
sudo ln -s /usr/local/bin/ccache /usr/local/bin/cc
sudo ln -s /usr/local/bin/ccache /usr/local/bin/c++
sudo ln -s /usr/local/bin/ccache /usr/local/bin/gcc
sudo ln -s /usr/local/bin/ccache /usr/local/bin/g++

I recommend to set its cache to 32GB

ccache --max-size 32G

Enjoy, you're gonna like it! :-)

Nil

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Austin

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Apr 3, 2019, 4:08:06 AM4/3/19

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Hi all,

Having installed all the 3 parts, this issue still persists

Traceback (most recent call last):

File "scheme_router.py", line 5, in <module>

from opencog.atomspace import types

ModuleNotFoundError: No module named 'opencog.atomspace'

I cant seem to use opencog.atomspace where-ever I try, whether with the python rest API or through guile

I have python installed and referenced in my .bashrc file as described

export PYTHONPATH="${PYTHONPATH}:/usr/local/lib/python3.6/dist-packages/opencog"

export PYTHONPATH="${PYTHONPATH}:/home/ubuntu/opencog/build/opencog/python/"

export PYTHONPATH="${PYTHONPATH}:/home/ubuntu/opencog/build/opencog/cython"

PYTHONPATH="$PYTHONPATH:/my/foo/bar"

export PYTHONPATH

Please why could this still be ????

Everything seems in place when I,

Run find /usr |grep opencog |grep python

/usr/local/share/guile/site/2.2/opencog/python.scm

/usr/local/lib/python3.6/dist-packages/opencog

/usr/local/lib/python3.6/dist-packages/opencog/statistics.so

/usr/local/lib/python3.6/dist-packages/opencog/web

/usr/local/lib/python3.6/dist-packages/opencog/web/api

/usr/local/lib/python3.6/dist-packages/opencog/web/api/restapi.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/apitypes.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/apighost.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/apischeme.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/apishell.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/apiatomcollection.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/apimain.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/mappers.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/__init__.py

/usr/local/lib/python3.6/dist-packages/opencog/web/api/utilities.py

/usr/local/lib/python3.6/dist-packages/opencog/web/socketio

/usr/local/lib/python3.6/dist-packages/opencog/web/socketio/atomspace_publisher.py

/usr/local/lib/python3.6/dist-packages/opencog/web/socketio/__init__.py

/usr/local/lib/python3.6/dist-packages/opencog/web/__init__.py

/usr/local/lib/python3.6/dist-packages/opencog/agent_finder.so

/usr/local/lib/python3.6/dist-packages/opencog/cogserver_type_constructors.so

/usr/local/lib/python3.6/dist-packages/opencog/__init__.py

/usr/local/lib/python3.6/dist-packages/opencog/cogserver.so

/usr/local/lib/python3/dist-packages/opencog

/usr/local/lib/python3/dist-packages/opencog/ure.so

/usr/local/lib/python3/dist-packages/opencog/scheme_wrapper.so

/usr/local/lib/python3/dist-packages/opencog/atomspace.so

/usr/local/lib/python3/dist-packages/opencog/type_constructors.so

/usr/local/lib/python3/dist-packages/opencog/logger.so

/usr/local/lib/python3/dist-packages/opencog/utilities.so

/usr/local/lib/python3/dist-packages/opencog/__init__.py

/usr/local/lib/python3/dist-packages/opencog/bindlink.so

Thank you so much for your help so far!!!

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