install yade on HPC

Asked by nobody on 2019-10-04

Hi all,

Recently, I am asking the technician at my university to help me to install YADE on the cluster. it seems he cannot install the CGAL module. as follows are the errors that he met when he installs Yade.

#################################
Here's the command I run:

cmake -DCMAKE_INSTALL_PREFIX=/packages/7x/yade/2018.02b -DENABLE_GUI=OFF -DENABLE_GTS=ON -DENABLE_VTK=OFF -DENABLE_PFVFLOW=OFF -DENABLE_TWOPHASEFLOW=OFF -DENABLE_CGAL=ON ..

Here's the output it provides back, omitting anything beyond CGAL's error:

-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/lib64/ccache/cc
-- Check for working C compiler: /usr/lib64/ccache/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/lib64/ccache/c++
-- Check for working CXX compiler: /usr/lib64/ccache/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /packages/7x/anaconda2/5.2.0/bin/python (found version "2.7.15")
-- Found OpenMP_C: -fopenmp (found version "3.1")
-- Found OpenMP_CXX: -fopenmp (found version "3.1")
-- Found OpenMP: TRUE (found version "3.1")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.5")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Version is set to 2018.02b
-- Found OpenGL: /usr/lib64/libGL.so
-- GTS using gts-config /packages/7x/gts/121130/bin/gts-config
-- Using GTS from /packages/7x/gts/121130
-- Found GL2PS: /usr/lib64/libgl2ps.so
-- CGAL not found.

Now, I have tried far more sophisticated approaches, by including these paths:

-DCGAL_INCLUDE_DIR
-DCGAL_LIBRARIES

Such as this attempt:

cmake -DCMAKE_INSTALL_PREFIX=/packages/7x/yade/2018.02b -DENABLE_GUI=OFF -DENABLE_GTS=ON -DENABLE_VTK=ON -DENABLE_PFVFLOW=OFF -DENABLE_TWOPHASEFLOW=OFF -DENABLE_CGAL=ON -DCGAL_DIR=/packages/7x/cgal/4.13.1 -DCGAL_INCLUDE_DIR=/packages/7x/cgal/4.13.1/include -DCGAL_LIBRARIES=/packages/7x/cgal/4.13.1/lib64 ..

-- Found CGAL

^ It "finds" cgal.... but errors out with:

[ 29%] Building CXX object CMakeFiles/yade.dir/pkg/common/common.cpp.o
In file included from /scratch/wdizon/builds/yade/241/src/lib/triangulation/Tesselation.h:9:0,
                 from /scratch/wdizon/builds/yade/241/src/pkg/dem/TesselationWrapper.hpp:15,
                 from /scratch/wdizon/builds/yade/241/src/pkg/common/PersistentTriangulationCollider.hpp:12,
                 from /scratch/wdizon/builds/yade/241/src/pkg/common/PersistentTriangulationCollider.cpp:9:
/scratch/wdizon/builds/yade/241/src/lib/triangulation/RegularTriangulation.h:11:64: fatal error: CGAL/Exact_predicates_inexact_constructions_kernel.h: No such file or directory
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
                                                                ^
compilation terminated.
make[2]: *** [CMakeFiles/yade.dir/pkg/common/PersistentTriangulationCollider.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from /scratch/wdizon/builds/yade/241/src/pkg/common/ZECollider.cpp:5:0:
/scratch/wdizon/builds/yade/241/src/pkg/common/ZECollider.hpp:19:37: fatal error: CGAL/box_intersection_d.h: No such file or directory
 #include <CGAL/box_intersection_d.h>
                                     ^
compilation terminated.

Does the file listed in the error above exist? Yes.

$ ls -la /packages/7x/cgal/4.13.1/include/CGAL/box_intersection_d.h
-rw-r--r-- 1 root root 16520 Mar 29 2019 /packages/7x/cgal/4.13.1/include/CGAL/box_intersection_d.h

#########################

is there anyone who can give us some suggestions.

best,
yong

Question information

Language:
English Edit question
Status:
Expired
For:
Yade Edit question
Assignee:
No assignee Edit question
Last query:
2019-10-08
Last reply:
2019-10-23
Robert Caulk (rcaulk) said : #1

Hello nobody,

Thanks for copying the error. But, without the linux version, we cannot help you.

Cheers,

Robert

Hi,
Try something like this?
-DCMAKE_CXX_FLAGS=-I/packages/7x/cgal/4.13.1/include

Bruno

nobody (nobody01) said : #3

Hi Robert,
here is the Linux version for our HPC.

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

best,
yong

nobody (nobody01) said : #4

Hi Robert,
here is the Linux version for our HPC.

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

best,
yong

Robert Caulk (rcaulk) said : #5

What happens when you try #2?

nobody (nobody01) said : #6

Hi Robert,

IT from my university is still working on this, so he didn't give me a response. once he gives me the response, I will post it here.

Launchpad Janitor (janitor) said : #7

This question was expired because it remained in the 'Open' state without activity for the last 15 days.