Yade

yade --check

Asked by azim

Dear all,

Here is my Problem. In running oedometer.py I got this result:

Qin= -7.87821707663e-07 Qout= 7.87395513513e-07.........>>>>> Qin is not completely equal to Qout.???

I thought it may be incorrect. because when I was running my script, I added FlowEngine to my simulation loop in ""Inspector"". It did not work, so I added TFlowEngine and it worked(I think so, at least I saw the movements of the particles). for being more sure about that:

I typed : "yade-2017-10-26.git-c434d0a --check" in Terminal and the results are as following:

Welcome to Yade 2017-10-26.git-c434d0a
###################################
running: checkLiquidMigration.py
This checkLiquidMigration.py cannot be executed because LIQMIGRATION is disabled
Status: success
___________________________________
###################################
Skipping checkList.py, because it is in SkipScripts
###################################
running: DEM-PFV-check.py
DEM-PFV: unbalanced Qin vs. Qout ( -4.06958960523e-06 vs. 4.06922520944e-06 )
(INFO) DEM-PFV: More than 60\% of cpu time in FlowEngine ( 97.3280306481 %). Should not happen with efficient libraries (check blas/lapack/cholmod implementations)
DEM-PFV-check.py failure
###################################
running: checkWeight.py
Precalculated weight 756.093387
Obtained weight 756.093387
Status: success
___________________________________
###################################
running: checkCapillaryModels.py
Status: success
___________________________________
###################################
running: checkViscElEng.py
Precalculated en value 0.736356797441
Obtained en value 0.736356797441
Status: success
___________________________________
###################################
running: checkPolyhedraCrush.py
Checkpoint: force values and number of bodies are OK! Iteration 250
Checkpoint: force values and number of bodies are OK! Iteration 300
Checkpoint: force values and number of bodies are OK! Iteration 310
Checkpoint: force values and number of bodies are OK! Iteration 330
Status: success
___________________________________
###################################
running: checkWirePM.py
Status: success
___________________________________
###################################
running: checkTestDummy.py
checkTest mechanism
Status: success
___________________________________
###################################
running: checkGravity.py
Status: success
___________________________________
###################################
running: checkClumpHopper.py
Iter 10000: Total number of generated spheres 1448, removed particles 0, current particles 1448, kinEnergy 21324.5
Iter 20000: Total number of generated spheres 2896, removed particles 157, current particles 2739, kinEnergy 50007.9
Iter 30000: Total number of generated spheres 3620, removed particles 812, current particles 2808, kinEnergy 39827.2
Iter 40000: Total number of generated spheres 5068, removed particles 1630, current particles 3438, kinEnergy 35535.8
Iter 50000: Total number of generated spheres 5068, removed particles 2111, current particles 2957, kinEnergy 27032.6
Status: success
___________________________________
###################################
running: checkViscElPM2.py
Status: success
___________________________________
###################################
running: checkViscElPM.py
Status: success
___________________________________
###################################
running: checkTestTriax.py
File ./checkTest.yade moved into /tmp/tmpBzsNYR/ directory
File ./_Unloaded_380_3.spheres moved into /tmp/tmpBzsNYR/ directory
File ./_Unloaded_380_3.xml moved into /tmp/tmpBzsNYR/ directory
File ./WallStresses moved into /tmp/tmpBzsNYR/ directory
Status: success
___________________________________
###################################
running: checkSaveLoadClumps.py
Status: success

Q1) I think there is a problem in DEM-PFV-check.py and checkLiquidMigration.py. any help for solving this problem is appreciated (if it is still a problem, I don't know yet)?

Q2) what is the difference between FlowEngine and FlowEngineT???

Q3)is there any reference for being more familiar with flowEngine family and their suitable applications?:
(FlowEngine.....FlowEngineT......DFNFlowEngine....FlowEngine_PeriodicInfo)

Thanks a lot for your help in advance.

Azim

Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Jérôme Duriez
Solved:
Last query:
Last reply:
Revision history for this message
Robert Caulk (rcaulk) said : 		#1

Hello Azim,

I gather you are compiling from sources? Which Linux release are you using?

>I added FlowEngine to my simulation loop in ""Inspector""

I do not recommend adding engines through the inspector. Add FlowEngine using scripting as shown in oedometer.py and DEM-PFV-check.py.

Q1) I think there is a problem in DEM-PFV-check.py and checkLiquidMigration.py. any help for solving this problem is appreciated (if it is still a problem, I don't know yet)?

LIQMIGRATION is not enabled in your compilation. It needs to be enabled in your compilation if you want to use it in Yade.

DEM-PFV appears to have some small problems. FlowEngine is being engaged; it passes most of the DEM-PFV tests (modulus, permeability, final pressure, deformation). The difference in Qin and Qout is so small...it is almost enough to neglect but I think it is worth investigating a bit further. Please :
*detail your installation method
*test yadedaily --check works fine
*make sure you have updated libmetis-dev and libsuitesparse-dev from packages
* run yadeXXX -jN --check where N is the number of cores on your computer

Q2) what is the difference between FlowEngine and FlowEngineT???

FlowEngineT should not be used directly [1]. It exists for inheritance purposes only.

Q3)is there any reference for being more familiar with flowEngine family and their suitable applications?:
(FlowEngine.....FlowEngineT......DNFFlowEngine....FlowEngine_PeriodicInfo)

Yes, the class reference [2].

[1]https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FlowEngineT
[2]https://yade-dem.org/doc/yade.wrapper.html

Revision history for this message
azim (mirzavand) said : 		#2

Hi Robert,

I am so grateful that you are helping me again.

>I gather you are compiling from sources? Which Linux release are you using?
yes, I did from sources. I am using Ubuntu 16.04

> I do not recommend adding engines through the inspector. Add FlowEngine using scripting as shown in oedometer.py and DEM-PFV-check.py.
I don't know the difference(you can tell me the difference or show me the path to get the answer), but I will do as you say.(you are more expert)

>LIQMIGRATION is not enabled in your compilation. It needs to be enabled in your compilation if you want to use it in Yade.
I want to work with DEM-PFV, if LIQMIGRATION is necessary for DEM-PFV,so please tell me how to enable it.

>*detail your installation method
my installation method is here[1]:
but here is a brief if it bother you to follow the link:

I installed the git package on my system:

git clone <email address hidden>:yade/trunk.git …….> /home/azim/trunk as usual

and added yade external ppa:

sudo add-apt-repository ppa:yade-users/external
sudo apt-get update

executed these commands:

sudo apt-get install cmake git freeglut3-dev libloki-dev \
libboost-all-dev fakeroot dpkg-dev build-essential g++ \
python-dev ipython python-matplotlib libsqlite3-dev python-numpy python-tk gnuplot \
libgts-dev python-pygraphviz libvtk6-dev python-numpy libeigen3-dev \
python-xlib python-pyqt5 pyqt5-dev-tools python-pyqt5.qtwebkit gtk2-engines-pixbuf python-argparse \
libqglviewer-dev python-imaging libjs-jquery python-sphinx python-git python-bibtex \
libxmu-dev libxi-dev libcgal-dev help2man libbz2-dev zlib1g-dev python-minieigen

installed mandatory package:

sudo apt-get install python-gts
sudo apt-get install libopenblas-dev libsuitesparse-metis-dev

I made the directory named ‘built’ as follow: /home/azim/trunk/built
then I called cmake to cofigure the simulation like this:

cmake -DCMAKE_INSTALL_PREFIX=/home/azim/trunk/built /home/azim/trunk
cmake -DCMAKE_INSTALL_PREFIX=/home/azim/trunk/built /home/azim/trunk

And finally:

make
make install

cd /home/azim/built//bins
./yade-2017-10-26.git-c434d0a

>*test yadedaily --check works fine
I did so, this is the result:
yadedaily: command not found

Q) does yadedaily work when installing from sources???

>*make sure you have updated libmetis-dev and libsuitesparse-dev from packages

of course i had this error during installation process:
E: Package 'libsuitesparse-metis-dev' has no installation candidate
how can I update them??
I tried "sudo apt-get install libsuitesparse-dev" and "sudo apt-get install libmetis-dev" but it made no difference.

>* run yadeXXX -jN --check where N is the number of cores on your computer
I did, it shows the same result as ''yadexxx --check" ,as I did before.(showed above)
Q) N is for my system,being curious, I tried N=4,8,9 but it works and shows the same result.how??

[1] https://answers.launchpad.net/yade/+question/662020

thanks again,

Azim

Revision history for this message
azim (mirzavand) said : 		#3

sorry,
Modification: N is 4 in my system

Revision history for this message
Robert Caulk (rcaulk) said : 		#4

Is there a reason you are compiling from sources instead of installing from packages?

>yadedaily: command not found

Please install yadedaily according to [1] and test yadedaily --check.

[1]https://yade-dem.org/doc/installation.html#packages

Revision history for this message
azim (mirzavand) said : 		#5

>Is there a reason you are compiling from sources instead of installing from packages?
No, There is no necessity.
should I uninstall the one compiled from sources? or these two are compatible? if they are? of course i will follow [1].
let me know please.

Revision history for this message
Robert Caulk (rcaulk) said : 		#6

Ok, in this case, I recommend installing from packages [1]. The installations will not interfere with each other. If you follow the directions of [1], it will install everything you need to run FlowEngine. You can then run yade by simply typing yadedaily.

[1]https://yade-dem.org/doc/installation.html#packages

Revision history for this message
azim (mirzavand) said : 		#7

I followed [1]:

sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >> /etc/apt/sources.list'
wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key add -
sudo apt-get update
sudo apt-get install yadedaily

this is the result:

sudo apt-get install yadedaily
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 yadedaily : Depends: libyadedaily (= 2017.01a-187d6cfc7f~xenial-1) but 2017.01a-1047722e9a~xenial-1 is to be installed
             Depends: python-yadedaily (= 2017.01a-187d6cfc7f~xenial-1) but 2017.01a-1047722e9a~xenial-1 is to be installed
E: Unable to correct problems, you have held broken packages.

I did all I knew, but could not solve it......

Revision history for this message
Robert Caulk (rcaulk) said : 		#8

Are you sure you are running 16.04 LTS? Perhaps you are running a different
distribution.

Please read through this thread [1] and let me know if you still run into
the same problem.

Also, are you able to simply run “sudo apt-get install yade”?

[1]https://answers.launchpad.net/yade/+question/466546

On Thu, Dec 28, 2017 at 5:32 PM azim <email address hidden>
wrote:

> Question #662276 on Yade changed:
> https://answers.launchpad.net/yade/+question/662276
>
> Status: Answered => Open
>
> azim is still having a problem:
> I followed [1]:
>
> sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >>
> /etc/apt/sources.list'
> wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key
> add -
> sudo apt-get update
> sudo apt-get install yadedaily
>
> this is the result:
>
> sudo apt-get install yadedaily
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
>
> The following packages have unmet dependencies:
> yadedaily : Depends: libyadedaily (= 2017.01a-187d6cfc7f~xenial-1) but
> 2017.01a-1047722e9a~xenial-1 is to be installed
> Depends: python-yadedaily (= 2017.01a-187d6cfc7f~xenial-1)
> but 2017.01a-1047722e9a~xenial-1 is to be installed
> E: Unable to correct problems, you have held broken packages.
>
> I did all I knew, but could not solve it......
>
> --
> You received this question notification because you are subscribed to
> the question.
>

Revision history for this message
Jérôme Duriez (jduriez) said : 		#9

Hi,

It is also to note, especially with respect to your other question https://answers.launchpad.net/yade/+question/662502, (this had not been done yet ?) that the "(INFO) DEM-PFV: More than 60\% of cpu time in FlowEngine ( 97.3280306481 %)" message you get from the PFV check script is from my point of view a strong sign of a problem in the (non-)installation of the libraries required by the PFV part of your yade version installed from source.

Jérôme

Revision history for this message
azim (mirzavand) said : 		#10

Dear Robert and Jerome,

I removed any installed yade on my system and, started installing from the beginning.

Here is my system features:
Linux azim-X450LCP 4.4.0-104-generic #127-Ubuntu SMP Mon Dec 11 12:16:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Distributor ID: Ubuntu
Description: Ubuntu 16.04.3 LTS
Release: 16.04
Codename: xenial

This is the procedure:
……………………………………………………………...
git clone <email address hidden>:yade/trunk.git
Cloning into 'trunk'...
remote: Counting objects: 88821, done.
remote: Compressing objects: 100% (38/38), done.
remote: Total 88821 (delta 15), reused 21 (delta 10), pack-reused 88773
Receiving objects: 100% (88821/88821), 71.29 MiB | 67.00 KiB/s, done.
Resolving deltas: 100% (66261/66261), done.
Checking connectivity... done.
…………………………………………………………………………………………………………………………..

sudo add-apt-repository ppa:yade-users/external
[sudo] password for azim:
 More recent version of various external packages, which are less functional or buggy in ubuntu repositories.
 More info: https://launchpad.net/~yade-users/+archive/ubuntu/external
Press [ENTER] to continue or ctrl-c to cancel adding it

gpg: keyring `/tmp/tmpv7ch7jog/secring.gpg' created
gpg: keyring `/tmp/tmpv7ch7jog/pubring.gpg' created
gpg: requesting key 6D76D006 from hkp server keyserver.ubuntu.com
gpg: /tmp/tmpv7ch7jog/trustdb.gpg: trustdb created
gpg: key 6D76D006: public key "Launchpad PPA for yade-users" imported
gpg: Total number processed: 1
gpg: imported: 1 (RSA: 1)
OK
.................................................................................................................................
azim@azim-X450LCP:~$ sudo apt-get update
Hit:1 https://repo.skype.com/deb stable InRelease
Get:2 http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease [17.5 kB]
Hit:3 http://archive.ubuntu.com/ubuntu xenial InRelease
Get:4 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB]
Ign:2 http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease
Hit:5 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu xenial InRelease
Get:6 http://archive.ubuntu.com/ubuntu xenial-backports InRelease [102 kB]
Hit:7 http://ppa.launchpad.net/jonathonf/python-3.6/ubuntu xenial InRelease
Get:8 http://archive.ubuntu.com/ubuntu xenial-security InRelease [102 kB]
Hit:9 http://ppa.launchpad.net/kubuntu-ppa/backports/ubuntu xenial InRelease
Get:10 http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease [17.5 kB]
Get:11 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP-11 Metadata [307 kB]
Ign:10 http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease
Hit:12 http://ppa.launchpad.net/noobslab/apps/ubuntu xenial InRelease
Hit:13 http://ppa.launchpad.net/stebbins/handbrake-releases/ubuntu xenial InRelease
Ign:14 http://ppa.launchpad.net/yade-users/external/ubuntu xenial InRelease
Get:15 http://archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 64x64 Icons [210 kB]
Get:16 http://archive.ubuntu.com/ubuntu xenial-updates/universe amd64 DEP-11 Metadata [185 kB]
Get:17 http://archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 64x64 Icons [265 kB]
Get:18 http://archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 DEP-11 Metadata [5,892 B]
Get:19 http://archive.ubuntu.com/ubuntu xenial-backports/universe amd64 DEP-11 Metadata [4,712 B]
Get:20 http://archive.ubuntu.com/ubuntu xenial-backports/main amd64 DEP-11 Metadata [3,328 B]
Get:21 http://archive.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [62.4 kB]
Get:22 http://archive.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 Icons [57.6 kB]
Get:23 http://archive.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [51.3 kB]
Get:24 http://archive.ubuntu.com/ubuntu xenial-security/universe DEP-11 64x64 Icons [80.2 kB]
Ign:25 http://ppa.launchpad.net/yade-users/external/ubuntu xenial Release
Ign:26 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:27 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:28 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:29 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:30 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:31 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:32 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:26 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:27 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:28 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:29 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:30 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:31 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:32 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:26 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:27 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:28 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:29 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:30 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:31 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:32 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:26 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:27 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:28 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:29 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:30 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:31 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:32 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:26 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:27 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:28 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:29 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:30 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:31 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:32 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Err:26 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
  404 Not Found
Ign:27 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:28 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:29 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:30 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:31 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:32 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Fetched 1,574 kB in 4min 41s (5,589 B/s)
Reading package lists... Done
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: GPG error: http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A9653F936FD5529
W: The repository 'http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease' is not signed.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: GPG error: http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 531EE72F4C9D234C
W: The repository 'http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease' is not signed.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: The repository 'http://ppa.launchpad.net/yade-users/external/ubuntu xenial Release' does not have a Release file.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
E: Failed to fetch http://ppa.launchpad.net/yade-users/external/ubuntu/dists/xenial/main/binary-amd64/Packages 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
……………………………………………………………………………………………………

sudo apt-get install cmake git freeglut3-dev libloki-dev \
> libboost-all-dev fakeroot dpkg-dev build-essential g++ \
> python-dev ipython python-matplotlib libsqlite3-dev python-numpy python-tk gnuplot \
> libgts-dev python-pygraphviz libvtk6-dev python-numpy libeigen3-dev \
> python-xlib python-pyqt5 pyqt5-dev-tools python-pyqt5.qtwebkit gtk2-engines-pixbuf python-argparse python-pyqt5.qtsvg \
> libqglviewer-dev python-imaging libjs-jquery python-sphinx python-git python-bibtex \
> libxmu-dev libxi-dev libcgal-dev help2man libbz2-dev zlib1g-dev python-minieigen
 Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libpython2.7-stdlib' instead of 'python-argparse'
build-essential is already the newest version (12.1ubuntu2).
fakeroot is already the newest version (1.20.2-1ubuntu1).
g++ is already the newest version (4:5.3.1-1ubuntu1).
libbz2-dev is already the newest version (1.0.6-8).
libjs-jquery is already the newest version (1.11.3+dfsg-4).
libsqlite3-dev is already the newest version (3.11.0-1ubuntu1).
libxi-dev is already the newest version (2:1.7.6-1).
libxmu-dev is already the newest version (2:1.1.2-2).
python-dev is already the newest version (2.7.11-1).
python-numpy is already the newest version (1:1.11.0-1ubuntu1).
python-tk is already the newest version (2.7.11-2).
freeglut3-dev is already the newest version (2.8.1-2).
gnuplot is already the newest version (4.6.6-3).
help2man is already the newest version (1.47.3).
ipython is already the newest version (2.4.1-1).
libboost-all-dev is already the newest version (1.58.0.1ubuntu1).
libcgal-dev is already the newest version (4.7-4).
libeigen3-dev is already the newest version (3.3~beta1-2).
libgts-dev is already the newest version (0.7.6+darcs121130-1.2).
libloki-dev is already the newest version (0.1.7-3ubuntu1).
libqglviewer-dev is already the newest version (2.6.3+dfsg1-1).
libvtk6-dev is already the newest version (6.2.0+dfsg1-10build1).
python-bibtex is already the newest version (1.2.7-1).
python-git is already the newest version (1.0.1+git137-gc8b8379-2.1).
python-matplotlib is already the newest version (1.5.1-1ubuntu1).
python-minieigen is already the newest version (0.50.3+dfsg1-4build1).
python-pygraphviz is already the newest version (1.3.1-0ubuntu2).
python-xlib is already the newest version (0.14+20091101-5).
cmake is already the newest version (3.5.1-1ubuntu3).
dpkg-dev is already the newest version (1.18.4ubuntu1.3).
git is already the newest version (1:2.7.4-0ubuntu1.3).
libpython2.7-stdlib is already the newest version (2.7.12-1ubuntu0~16.04.2).
zlib1g-dev is already the newest version (1:1.2.8.dfsg-2ubuntu4.1).
gtk2-engines-pixbuf is already the newest version (2.24.30-1ubuntu1.16.04.2).
python-imaging is already the newest version (3.1.2-0ubuntu1.1).
python-sphinx is already the newest version (1.3.6-2ubuntu1.1).
pyqt5-dev-tools is already the newest version (5.5.1+dfsg-3ubuntu5~xenialoverlay11~1).
python-pyqt5 is already the newest version (5.5.1+dfsg-3ubuntu5~xenialoverlay11~1).
python-pyqt5.qtwebkit is already the newest version (5.5.1+dfsg-3ubuntu5~xenialoverlay11~1).
python-pyqt5.qtsvg is already the newest version (5.5.1+dfsg-3ubuntu5~xenialoverlay11~1).
The following package was automatically installed and is no longer required:
  libllvm4.0
Use 'sudo apt autoremove' to remove it.
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
…………………………………………………………………………………………………………………..

sudo apt-get install python-gts
Reading package lists... Done
Building dependency tree
Reading state information... Done
python-gts is already the newest version (0.3.1-6).
The following package was automatically installed and is no longer required:
  libllvm4.0
Use 'sudo apt autoremove' to remove it.
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
……………………………………………………………………………………………………………..
sudo apt-get install libopenblas-dev libsuitesparse-metis-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package libsuitesparse-metis-dev is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
  libsuitesparse-dev:i386 libsuitesparse-dev

E: Package 'libsuitesparse-metis-dev' has no installation candidate
……………………………………………………………………………………………………………...

###################################################
QQ) PLEASE: help me to solve above errors.
after solving them, I want to start compilation.
any comment about DEM-PFV packages is welcomed.

I really really really, appreciate your help
thanks

Azim

Revision history for this message
Robert Caulk (rcaulk) said : 		#11

Hello Azim,

Please, help me help you get Yade installed on your machine :-) I will reiterate my past responses here.

It appears to me that you are mixing up installation procedures. There are several ways to install yade, each method is highlighted here [1]. You do not need to install yade with all methods indicated in that document, you only need to choose one method. The most straightforward way is to use "packaged" installation.

We came to the conclusion earlier in this thread that your best bet will be to install yadedaily from packages. So you only need to follow the first few instructions in the "pacakges" [2] section:

sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >> /etc/apt/sources.list'
wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key add -
sudo apt-get update
sudo apt-get install yadedaily

It appears you tried this at some point in the thread, but you ran into an error with one of the libraries. I searched the Yade forums for the same error and came upon this thread [3], which seems to suggest you may have typed one of the commands incorrectly. I implore(d) you to read through [3] to see if that problem aligns with yours, and maybe the solution aligns with yours as well.

I also asked if you are able to simply type "sudo apt-get install yade" ? But I never heard a response...

Cheers,

Robert

[1]https://yade-dem.org/doc/installation.html#installation
[2]https://yade-dem.org/doc/installation.html#packages
[3]https://answers.launchpad.net/yade/+question/466546

Revision history for this message
azim (mirzavand) said : 		#12

Hi Robert,

i have tried thread[1] over and over in last 3 days. and I got the same result.I followed it in a few minutes ago and this is the result after installing:

INSTALLING YADEDAILY

sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >> /etc/apt/sources.list'
[sudo] password for azim:
azim@azim-X450LCP:~$ wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key add -
--2018-01-05 07:45:30-- http://www.yade-dem.org/packages/yadedev_pub.gpg
Resolving www.yade-dem.org (www.yade-dem.org)... 194.254.65.201
Connecting to www.yade-dem.org (www.yade-dem.org)|194.254.65.201|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3143 (3.1K)
Saving to: ‘STDOUT’

- 100%[===================>] 3.07K --.-KB/s in 0s

2018-01-05 07:45:34 (54.2 MB/s) - written to stdout [3143/3143]

OK
azim@azim-X450LCP:~$ sudo apt-get update
Get:1 http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease [17.5 kB]
Get:2 http://www.yade-dem.org/packages xenial/ InRelease [2,460 B]
Get:3 http://www.yade-dem.org/packages xenial/ Packages [2,187 B]
Ign:1 http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease
Hit:4 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu xenial InRelease
Hit:5 http://ppa.launchpad.net/jonathonf/python-3.6/ubuntu xenial InRelease
Hit:6 https://repo.skype.com/deb stable InRelease
Hit:7 http://archive.ubuntu.com/ubuntu xenial InRelease
Hit:8 http://ppa.launchpad.net/kubuntu-ppa/backports/ubuntu xenial InRelease
Hit:9 http://archive.ubuntu.com/ubuntu xenial-updates InRelease
Get:10 http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease [17.5 kB]
Hit:11 http://archive.ubuntu.com/ubuntu xenial-backports InRelease
Hit:12 http://archive.ubuntu.com/ubuntu xenial-security InRelease
Ign:10 http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease
Hit:13 http://ppa.launchpad.net/noobslab/apps/ubuntu xenial InRelease
Hit:14 http://ppa.launchpad.net/stebbins/handbrake-releases/ubuntu xenial InRelease
Ign:15 http://ppa.launchpad.net/yade-users/external/ubuntu xenial InRelease
Ign:16 http://ppa.launchpad.net/yade-users/external/ubuntu xenial Release
Ign:17 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:18 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:19 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:20 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:21 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:22 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:23 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:17 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:18 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:19 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:20 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:21 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:22 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:23 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:17 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:18 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:19 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:20 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:21 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:22 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:23 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:17 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:18 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:19 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:20 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:21 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:22 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:23 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Ign:17 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
Ign:18 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:19 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:20 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:21 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:22 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:23 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Err:17 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 Packages
  404 Not Found
Ign:18 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main i386 Packages
Ign:19 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main all Packages
Ign:20 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en_US
Ign:21 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main Translation-en
Ign:22 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:23 http://ppa.launchpad.net/yade-users/external/ubuntu xenial/main DEP-11 64x64 Icons
Fetched 39.7 kB in 1min 21s (486 B/s)
Reading package lists... Done
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: GPG error: http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 6A9653F936FD5529
W: The repository 'http://ppa.launchpad.net/atareao/telegram/ubuntu xenial InRelease' is not signed.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: GPG error: http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 531EE72F4C9D234C
W: The repository 'http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease' is not signed.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: The repository 'http://ppa.launchpad.net/yade-users/external/ubuntu xenial Release' does not have a Release file.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
E: Failed to fetch http://ppa.launchpad.net/yade-users/external/ubuntu/dists/xenial/main/binary-amd64/Packages 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list.d/skype-stable.list:1 and /etc/apt/sources.list.d/skypeforlinux.list:1
azim@azim-X450LCP:~$ sudo apt-get install yadedaily
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following package was automatically installed and is no longer required:
  libllvm4.0
Use 'sudo apt autoremove' to remove it.
The following additional packages will be installed:
  libyadedaily python-yadedaily
The following NEW packages will be installed:
  libyadedaily python-yadedaily yadedaily
0 upgraded, 3 newly installed, 0 to remove and 1 not upgraded.
Need to get 12.9 MB of archives.
After this operation, 87.4 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://www.yade-dem.org/packages xenial/ libyadedaily 2017.01a-187d6cfc7f~xenial-1 [9,207 kB]
Get:2 http://www.yade-dem.org/packages xenial/ python-yadedaily 2017.01a-187d6cfc7f~xenial-1 [2,104 kB]
Get:3 http://www.yade-dem.org/packages xenial/ yadedaily 2017.01a-187d6cfc7f~xenial-1 [1,626 kB]
Fetched 12.9 MB in 3min 30s (61.5 kB/s)
Selecting previously unselected package libyadedaily:amd64.
(Reading database ... 276193 files and directories currently installed.)
Preparing to unpack .../libyadedaily_2017.01a-187d6cfc7f~xenial-1_amd64.deb ...
Unpacking libyadedaily:amd64 (2017.01a-187d6cfc7f~xenial-1) ...
Selecting previously unselected package python-yadedaily.
Preparing to unpack .../python-yadedaily_2017.01a-187d6cfc7f~xenial-1_amd64.deb ...
Unpacking python-yadedaily (2017.01a-187d6cfc7f~xenial-1) ...
Selecting previously unselected package yadedaily.
Preparing to unpack .../yadedaily_2017.01a-187d6cfc7f~xenial-1_amd64.deb ...
Unpacking yadedaily (2017.01a-187d6cfc7f~xenial-1) ...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for desktop-file-utils (0.22-1ubuntu5.1) ...
Processing triggers for bamfdaemon (0.5.3~bzr0+16.04.20160824-0ubuntu1) ...
Rebuilding /usr/share/applications/bamf-2.index...
Processing triggers for gnome-menus (3.13.3-6ubuntu3.1) ...
Processing triggers for mime-support (3.59ubuntu1) ...
Setting up libyadedaily:amd64 (2017.01a-187d6cfc7f~xenial-1) ...
Setting up python-yadedaily (2017.01a-187d6cfc7f~xenial-1) ...
Setting up yadedaily (2017.01a-187d6cfc7f~xenial-1) ...
#########################################

YADE --CHECK
yadedaily --check
Welcome to Yade 2017.01a-187d6cfc7f~xenial
###################################
running: checkLiquidMigration.py
This checkLiquidMigration.py cannot be executed because LIQMIGRATION is disabled
Status: success
___________________________________
###################################
Skipping checkList.py, because it is in SkipScripts
###################################
running: DEM-PFV-check.py
DEM-PFV: unbalanced Qin vs. Qout ( -0.00279199571618 vs. 0.0 )
DEM-PFV: difference in permeability: 27.9199571618 vs. target 0.040399916554
The difference is more, than the critical tolerance!
DEM-PFV: difference in final pressure: 0.0 vs. target 628.314160434
The difference is more, than the critical tolerance!
DEM-PFV: difference in final deformation -0.00430506304298 vs. target -0.00258113045083
The difference is more, than the critical tolerance!
DEM-PFV: Metis is not used during cholmod's reordering although explicitly enabled, something wrong with libraries
Status: FAILURE!!!
___________________________________
###################################
running: checkWeight.py
Precalculated weight 756.093387
Obtained weight 756.093387
Status: success
___________________________________
###################################
running: checkCapillaryModels.py
Status: success
___________________________________
###################################
running: checkViscElEng.py
Precalculated en value 0.736356797441
Obtained en value 0.736356797441
Status: success
___________________________________
###################################
running: checkPolyhedraCrush.py
Checkpoint: force values and number of bodies are OK! Iteration 250
Checkpoint: force values and number of bodies are OK! Iteration 300
Checkpoint: force values and number of bodies are OK! Iteration 310
Checkpoint: force values and number of bodies are OK! Iteration 330
Status: success
___________________________________
###################################
running: checkWirePM.py
Status: success
___________________________________
###################################
running: checkTestDummy.py
checkTest mechanism
Status: success
___________________________________
###################################
running: checkGravity.py
Status: success
___________________________________
###################################
running: checkClumpHopper.py
Iter 10000: Total number of generated spheres 1448, removed particles 0, current particles 1448, kinEnergy 13755.3
Iter 20000: Total number of generated spheres 2896, removed particles 157, current particles 2739, kinEnergy 32441.5
Iter 30000: Total number of generated spheres 3620, removed particles 812, current particles 2808, kinEnergy 25812.6
Iter 40000: Total number of generated spheres 5068, removed particles 1630, current particles 3438, kinEnergy 23692.9
Iter 50000: Total number of generated spheres 5068, removed particles 2111, current particles 2957, kinEnergy 17471
Status: success
___________________________________
###################################
running: checkViscElPM2.py
Status: success
___________________________________
###################################
running: checkViscElPM.py
Status: success
___________________________________
###################################
running: checkTestTriax.py
File ./checkTest.yade moved into /tmp/tmpob1NXn/ directory
File ./_Unloaded_380_3.spheres moved into /tmp/tmpob1NXn/ directory
File ./_Unloaded_380_3.xml moved into /tmp/tmpob1NXn/ directory
File ./WallStresses moved into /tmp/tmpob1NXn/ directory
Status: success
___________________________________
###################################
running: checkSaveLoadClumps.py
Status: success
___________________________________
1 tests are failed
---------------------------------------------------------------------------------------------------------------------

What is my problem??

Revision history for this message
Jérôme Duriez (jduriez) said : 		#13

Hi Azim,

I think I successfully installed from sources a PFV-enabled yade, yesterday.
To do so, I think I installed the following packages:

- libmetis-dev
- libmetis5
- libsuitesparse-dev

I think these replace the probably outdated (for Ubuntu 16.04)"sudo apt-get install libopenblas-dev libsuitesparse-metis-dev" of current https://yade-dem.org/doc/installation.html, which by the way made you face some problems.

I have no idea whether such manual installation of external packages is also necessary for installation of yade / yadedaily packaged versions.

Jérôme

Revision history for this message
Jérôme Duriez (jduriez) said : 		#14

My previous message was maybe too optimistic...

While the above mentioned packages allowed me

- to get, at cmake stage
"
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
" (instead of getting some of them "not found")

- and have "examples/FluidCouplingPFV/oedometer.py" showing a "Gauss-Seidel" partial time of "FlowEngine" decreasing (after installing these packages) from ~ 99% to 49%

I also get a failure at DEM-PFV-check.py (after launching check tests on this yade version):

###################################
running: DEM-PFV-check.py
DEM-PFV: unbalanced Qin vs. Qout ( -0.00279199571618 vs. 0.0 )
DEM-PFV: difference in permeability: 27.9199571618 vs. target 0.040399916554
The difference is more, than the critical tolerance!
DEM-PFV: difference in final pressure: 0.0 vs. target 628.314160434
The difference is more, than the critical tolerance!
DEM-PFV: difference in final deformation -0.00430506304298 vs. target -0.00258113045083
The difference is more, than the critical tolerance!
DEM-PFV: Metis is not used during cholmod's reordering although explicitly enabled, something wrong with libraries
Status: FAILURE!!!
####################################

(same as you, Azim ?)

I'm afraid other answers would be necessary (problem is, the discussion is kind of untractable...)

Revision history for this message
Bruno Chareyre (bruno-chareyre) said : 		#15

Hi,
I can reproduce #14.
It is odd: if I run manually the same script used for the --check, with the command
yadedaily DEM-PFV-check.py
then it gives the expected results.
The oedometer.py example also give expected behavior. I thus guess you both have working versions installed despite the apparent --check failure.
Bruno

Revision history for this message
Bruno Chareyre (bruno-chareyre) said : 		#16

Back to the original statement:
"Qin= -7.87821707663e-07 Qout= 7.87395513513e-07.........>>>>> Qin is not completely equal to Qout.???"

They cannot be equal since:
1- they result from a (lot of) calculations which all generate numerical errors, including the Cholesky factorization of a linear system.
2- they are theoretically equal only if the solid phase is fixed, in the script there is a residual momentum resulting from the compaction phase.
The difference is of the order of 5e-4*Q. That's quite ok given 1/ and 2/

Bruno

Revision history for this message
azim (mirzavand) said : 		#17

Hi Bruno

> The difference is of the order of 5e-4*Q. That's quite ok given 1/ and 2/
It's OK.

I tried all ways of yade installation recently. I even reinstalled Ubuntu on my system(SO beginner).
now, i'm using ubuntu 14.04 trusty. and yade installed from packages.

Q1) how can i solve (running: DEM-PFV-check.py, Status: FAILURE!!!)?

Q2) suppose that we ignore the yadedaily --check results.(OK?) IF FlowEngine exists in my simulation!! why does FlowEngine.ids return []???? what does it mean??? is it saying that flow does not exert on the particles?

thank you,
Azim

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Best Jérôme Duriez (jduriez) said : 		#18

Hi

Q1) No need for you to try to solve this.
According to #15, it is more a problem in the definition of the --check procedure, thus a general problem in YADE. You may try examples/FluidCouplingPFV/oedometer.py (which has an analytical expected solution) to check whether FlowEngine works on your computer

Q2) As suggested by the doc [1], FlowEngine.ids is derived from PartialEngine.ids [2], see the inheritance (see c++ concepts) diagram at [3].
However I do not think this ids variable actually has any role in the workflow of FlowEngine. I would say that the fact FlowEngine.ids is empty is thus harmless, see Q1 again to be sure FlowEngine works on your computer.
If you're really curious about this FlowEngine.ids and why FlowEngine is defined as a PartialEngine, and not a GlobalEngine, please open a new question: it is completely unrelated with yade --check, now.

[1] https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FlowEngine.ids
[2] https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.PartialEngine.ids
[3] https://yade-dem.org/doc/yade.wrapper.html#partial-engines

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azim (mirzavand) said : 		#19

Hi Jerome,

>If you're really curious about this FlowEngine.ids and why FlowEngine is defined as a PartialEngine, and not a GlobalEngine, please open a new question: it is completely unrelated with yade --check, now.
i will follow you'r suggestion.
thanks

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azim (mirzavand) said : 		#20

Thanks Jérôme Duriez, that solved my question.