TELEMAC-MASCARET Forum: step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel (4/8)

step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25217

stef

One more thing, i had a problem today with a computer and an previously installed paraview, which is link to openmpi with ubuntu. SO i tried to compile a specific mpich for telemac and it works ! (url=https://researchweb.iiit.ac.in/~abu_saad/files/Installing_MPI.pdf]MPI install manual from here[/url])

download and prepare

cd ~/telemac/v7p2/optionals
mkdir mpich
cd mpich
wget http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
tar xfz mpich-3.2.tar.gz
mkdir mpich-install
mkdir mpich
cd mpich

replace XXXXXXX with your ubuntu login, no relative path is possible

~/telemac/v7p2/optionals/mpich/mpich-3.2/configure -prefix=/home/XXXXXXX/telemac/v7p2/optionals/mpich/mpich-install

make
make install

and the .cfg file :

File Attachment:

File Name: systel.ubuntu_2017-02-13-2.cfg
File Size: 3 KB

Once again, those kind of compile/install is pretty new for me, and configure the .cfg file for telemac is not so simple...

Hope it helps !

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step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25219

yugi OFFLINE openTELEMAC Guru Posts: 851 Thank you received: 244	Hi, You can find a new guide for installation here: wiki.opentelemac.org/doku.php?id=installation_notes_2_beta Tell me what you think of it.
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step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25285

stef	Hello Yugi, it is far better than the install documentation on the website of Telemac, and it will help beginners I think. Just take care that the install scripts that I wrote are not "linux" scripts, but "debian" scripts. For example, sudo apt-get install XXXX is urpmi XXXX within Mandriva/Mageia and yum install XXXX within Fedora
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step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25294

yugi OFFLINE openTELEMAC Guru Posts: 851 Thank you received: 244	Very good remark I'll correct that. By the way it will replace the documentation installation on the website.
	There are 10 types of people in the world: those who understand binary, and those who don't. The administrator has disabled public write access.

step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 9 months ago #25354

stef

I finally managed to install Telemac onto Ubuntu 16.04 with a full intel solution (ifort, metis compiled with ifort, and mpi from intel parallel studio 2017). Performances are really better than gfortran-mpich, and better than ifort-mpich compiled with ifortran. I will post the step-by-step guide soon and some benchmarks.

Just a question, has someone try to use intel distribution for python ? Can it improve performance as well ?

Thanks for the answer.

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step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 9 months ago #25359

josekdiaz
OFFLINE
Expert Boarder
Posts: 161
Thank you received: 48

Dear Stef,

Really glad to hear that! I do have a telemac build of Intel's mpi + ifort functional but got a feeling that it behaves incorrectly somehow, so I will test with your config and report back! (I have a parallel cluster 2016 to play around).

Also didn't know that intel had its own python distro and surely must run faster, but have my doubts about numpy and scipy because AFAIK the binaries that are packaged within linux repos have been already been compiled with intel's dev kit, so there shouldnt been much diference, at least with those two...

regards,

José Díaz.

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step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25394

stef

Hello, here is the step by step guide to install telemac with intel parallel studio 2017 update 2 (feb. 2017) on ubuntu 16.04 (may work on debian, but not tested). I have tested it on virtual machine with virtual box, and my computer (i7-2600K proc.), within Ubuntu 16.04.

First of all download intel parallel studio from here. It's free for students and developpers.

The guide is made with the online file of intel, but you can download the huge (4 Go) offline file if you want, but it still needs a connection to activate licence, and the intel components needed for telemac are only 600 Mo, so i prefer online procedure.

Then, let's go.

install dependencies

sudo apt-get update && sudo apt-get upgrade
sudo apt-get install -y rpm build-essential subversion vim cmake python python-numpy dialog

download telemac

svn co http://svn.opentelemac.org/svn/opentelemac/tags/v7p2r0/  ~/telemac/v7p2 --username ot-svn-public --password telemac1*

prepare installation of intel studio

cd ~/telemac/v7p2/optionals
mkdir tmp
cd tmp

place in /tmp intel file parallel_studio_xe_2017... and do

tar xvzf parallel_studio_xe_2017_update2_cluster_edition_online.tgz
cd parallel_studio_xe_2017_update2_cluster_edition_online

install intel fortran, intel c++ and intel mpi in GUI mode [in option, write a silent_telemac.cfg file to to do it again without human confirmation]

./install_GUI.sh [--duplicate=silent_telemac.cfg]

graphical steps : choose install as root using sudo mode, install on this computer, accept licence, enter serial number, install on this computer only,
CUSTOMIZE, don't modify path, next, TICK (SELECT) ONLY 64 bits - (Intel 64), CHOOSE C++, fortran, MPI (deselect all, than select the components, take care, the dialog box is very slow to take your click into account)

An alternative : install intel fortran, intel c++ and intel mpi in CLI mode [with existing silent file]

sudo ./install.sh [--silent=silent_telemac.cfg]

bashrc settings

vim ~/.bashrc

then insert these lines with "i" at the end of the file

# telemac
export PATH=~/telemac/v7p2/scripts/python27/:$PATH
export SYSTELCFG=~/telemac/v7p2/configs/systel.ubuntu.cfg
# intel fortran
export PATH=/opt/intel/bin:$PATH
LD_LIBRARY_PATH=/opt/intel/lib/intel64
export LD_LIBRARY_PATH
export I_MPI_F90=ifort

escape (ESC) save with":wq" + RETURN.
Apply with

source ~/.bashrc

At that time you can check your installation :

ifort --version
icc --version
icpc --version

download and compile metis 5.1.0

cd ~/telemac/v7p2/optionals
rm -rf metis-5.1.0
mkdir tmp
cd tmp
wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
tar xzf metis-5.1.0.tar.gz
cp -r metis-5.1.0 ~/telemac/v7p2/optionals/
cd ~/telemac/v7p2/optionals/metis-5.1.0
vim Makefile

change ("i" then ESC then ":wq")

prefix = ~/telemac/v7p2/optionals/metis-5.1.0/build/
cc = icc

compile

make config
make

copy systel.ubuntu.cfg into ~/telemac/v7p2/configs/

File Attachment:

File Name: systel.ubuntu_2017-02-25.cfg
File Size: 2 KB

Please notice that I did not managed (telemac failed to compile) to install both intel mpi (parallel) and ifortran (scalar) at the same time, but is it really useful ?

compile TELEMAC

compileTELEMAC.py

test it small

cd ~/telemac/v7p2/examples/telemac2d/bumpflu
telemac2d.py t2d_bumpflu.cas
telemac2d.py t2d_bumpflu.cas --ncsize=4

test it large

cd ~/telemac/v7p2/examples/telemac2d/malpasset
telemac2d.py t2d_malpasset-large.cas --ncsize=4

Hope it helps, give me some precise questions if you want some help (i will try), be nice and improve my scripts and .cfg file if you want, but please DO NOT say "it does not work" ! (it is just actually working...).

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step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25396

stef	You can see benchmarks of my tests here.
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step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25416

stef

Hello, in fact it seems to have a problem with metis compiling with intel parallel studio 2017 update 2.

I give me some openMP pragma errors :

/home/telemac/telemac/v7p2/optionals/metis-5.1.0/GKlib/csr.c(796): error #3180: unrecognized OpenMP #pragma
        #pragma omp parallel private(i, j, ncand, rsum, tsum, cand)
                ^

So I try to compile metis with this makefile options :

openmp     = 1
prefix     = ~/telemac/v7p2/optionals/metis-5.1.0/build/
cc = icc

running

make config

gives me

rm -rf build/Linux-x86_64
mkdir -p build/Linux-x86_64
cd build/Linux-x86_64 && cmake /home/telemac/telemac/v7p2/optionals/metis-5.1.0 -DCMAKE_VERBOSE_MAKEFILE=1 -DGKLIB_PATH=/home/telemac/telemac/v7p2/optionals/metis-5.1.0/GKlib -DOPENMP=1 -DCMAKE_INSTALL_PREFIX=~/telemac/v7p2/optionals/metis-5.1.0/build/ -DCMAKE_C_COMPILER=icc 
-- The C compiler identification is Intel 17.0.2.20170213
-- The CXX compiler identification is Intel 17.0.2.20170213
-- Check for working C compiler: /opt/intel/bin/icc
-- Check for working C compiler: /opt/intel/bin/icc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /opt/intel/bin/icpc
-- Check for working CXX compiler: /opt/intel/bin/icpc -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Try OpenMP C flag = [-qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -qopenmp  
-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for getline
-- Looking for getline - found
-- checking for thread-local storage - found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/telemac/telemac/v7p2/optionals/metis-5.1.0/build/Linux-x86_64

And then, no problem with

make

The compilation of telemac gives me a lot or warnings, like

/home/telemac/telemac/v7p2/sources/utils/hermes/utils_med.F(2738): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.   [IERR]
      SUBROUTINE IDENTIFY_BND_ELMT(FILE_ID,TYPE_BND_ELEM,IERR)

   - completed: .../v7p2/sources/utils/splitsel/splitsel.f                     
ar: le modificateur « u » est ignoré puisque « D » est le défaut (consultez « U »)
   - completed: .../v7p2/builds/ubuimpi/lib/utils/special/splitsel.a
ar: le modificateur « u » est ignoré puisque « D » est le défaut (consultez « U »)

/home/telemac/telemac/v7p2/sources/mascaret/Fox/wkml/m_wkml_coverage.F90(8): remark #6536: All symbols from this module are already visible due to another USE; the ONLY clause will have no effect. Rename clauses, if any, will be honored.   [M_COMMON_ERROR]
  use m_common_error, only: FoX_error

/home/telemac/telemac/v7p2/sources/mascaret/Modules/m_profil_t.f90(29): warning #6379: The structure contains one or more misaligned fields.   [PROFIL_T]
  TYPE PROFIL_T
-------^

/home/telemac/telemac/v7p2/sources/mascaret/Deriv/diff_z_cf12_bwd_sarap.f90(4576): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.   [DZPREV]
& profil, profil_plan, numconfluence, connect, modelelit, epsil, dzprev&
-----------------------------------------------------------------^
/home/telemac/telemac/v7p2/sources/mascaret/Deriv/diff_z_cf12_fwd_sarap.f90(2245): warning #6379: The structure contains one or more misaligned fields.   [CONF_T]
  TYPE CONF_T
-------^
/home/telemac/telemac/v7p2/sources/mascaret/Deriv/diff_z_cf12_bwd_sarap.f90(6794): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.   [FROUDE]
& , rh1, rh1b, rh2, rh2b, s1, s1b, s2, s2b, beta, betab, froude, &
---------------------------------------------------------^

   - completed: .../v7p2/sources/mascaret/ModelesQualEau/calcs_thermic.f90     
/home/telemac/telemac/v7p2/sources/mascaret/N2QN1/n2qn1.f(479): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
 1019     format (/1x,i6,2x,i6,2x,i6,2x,1pe12.5,2x,es12.6)
-----------------------------------------------------^
/home/telemac/telemac/v7p2/sources/mascaret/N2QN1/n2qn1.f(796): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
          if (iprint.ge.4) write (lp,'(/1x,a,1pd8.2)')
------------------------------------------------^

   - completed: .../v7p2/sources/tomawac/rpi_invr.f                            
/home/telemac/telemac/v7p2/sources/tomawac/angles.f(109): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
     &       '/!/  THE VALUE HERE IMPOSED IS : ', G10.4,'       /!/'/
---------------------------------------------------^
/home/telemac/telemac/v7p2/sources/tomawac/angles.f(100): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
     &       '/!/  OR LA VALEUR UTILISEE EST : ', G10.4,'       /!/'/
---------------------------------------------------^

   - completed: .../v7p2/builds/ubuimpi/lib/utils/bief/homere_tomawac.a
ar: le modificateur « u » est ignoré puisque « D » est le défaut (consultez « U »)
   - completed: .../v7p2/builds/ubuimpi/lib/tomawac/homere_tomawac.a
   - created .../v7p2/builds/ubuimpi/bin/tomawac

but the compilation works.
Could someone help me to compile without warnings ?

I have strangely fast results with malpasset test case, 220s with 7 cores within virtual box, instead of 356s with intel parralel studio upt 1...

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step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25533

huyquangtran
OFFLINE
Expert Boarder
Posts: 271
Thank you received: 23

Hello,

I am also testing a new configuration with intel 2017. If I run TELEMAC 3D and TOMAWAC separately, INTEL done the job quicker than OpenMPI. However, I got an error message below..(actually the run suddenly stopped after 2nd step) when carrying out a coupled model TOMAWAC/TELEMAC, and I am still searching the way to tackle it.

It would be great if someone has experience in solving this problem to share with me.

Thanks in advance.

Best Regards
Huy

NUMBER OF SUB-ITERATIONS : 12
NUMBER OF SUB-ITERATIONS : 11
NUMBER OF SUB-ITERATIONS : 9

================================================================================
TEMPS : 1800.0000 SECONDES 60IEME ITERATION

LIMWAC: INTERPOLATION PASS
AT1= 0.0s, Hm1= 1.14m, DirN1= 14.3deg, Fpi1= 0.090Hz
AT2= 1800.0s, Hm2= 1.11m, DirN2= 17.3deg, Fpi2= 0.090Hz
BOUNDARY WAVE CONDIT: HM0= 1.11m, DIRN= 17.3deg, FPI= 0.090Hz

CALCUL DU CHAMP CONVECTEUR ET REMONTEE DES
CARACTERISTIQUES
NUMBER OF SUB-ITERATIONS : 27
NUMBER OF SUB-ITERATIONS : 25
NUMBER OF SUB-ITERATIONS : 24
NUMBER OF SUB-ITERATIONS : 22
NUMBER OF SUB-ITERATIONS : 20
NUMBER OF SUB-ITERATIONS : 18
NUMBER OF SUB-ITERATIONS : 16
NUMBER OF SUB-ITERATIONS : 15
NUMBER OF SUB-ITERATIONS : 13
NUMBER OF SUB-ITERATIONS : 12
NUMBER OF SUB-ITERATIONS : 11
NUMBER OF SUB-ITERATIONS : 9
INTERPOLATION AUX PIEDS DES CARACTERISTIQUES

PRISE EN COMPTE DES TERMES SOURCES EN 1 SOUS-ITERATION(S)

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 17570 RUNNING AT spartan-bm003
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
Intel(R) MPI Library troubleshooting guide:
software.intel.com/node/561764
===================================================================================
_____________
runcode::main:
:
|runCode: Fail to run
|/usr/local/easybuild/software/ifort/2017.u2-GCC-6.2.0/impi/2017.2.174/bin64/mpiexec -wdir /home/huyquangtran/telemac/3D_NEW_DATA/CUTEST.cas_2017-03-06-09h09min58s -n 8 /home/huyquangtran/telemac/3D_NEW_DATA/CUTEST.cas_2017-03-06-09h09min58s/out_IP_tide_windV
|~~~~~~~~~~~~~~~~~~
|Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
|
|Backtrace for this error:
|
|Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
|
|Backtrace for this error:
|#0 0x2AB020BAC6F7
|#1 0x2AB020BACD3E
|#2 0x2AB02163E66F
|#0 0x2B2B45A7B6F7
|#1 0x2B2B45A7BD3E
|#2 0x2B2B4650D66F
|#3 0x51B70B in ecrspe_
|#3 0x51B70B in ecrspe_
|#4 0x501C54 in wac_
|#4 0x501C54 in wac_
|#5 0x43C596 in telemac3d_
|#5 0x43C596 in telemac3d_
|#6 0x407705 in MAIN__ at homere_telemac3d.f:?
|#6 0x407705 in MAIN__ at homere_telemac3d.f:?
|
|Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
|
|Backtrace for this error:
|
|Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
|
|Backtrace for this error:
|#0 0x2B62739C56F7
|#1 0x2B62739C5D3E
|#2 0x2B627445766F
|#3 0x51B70B in ecrspe_
|#4 0x501C54 in wac_
|#5 0x43C596 in telemac3d_
|#6 0x407705 in MAIN__ at homere_telemac3d.f:?
|#0 0x2AD81327B6F7
|#1 0x2AD81327BD3E
|#2 0x2AD813D0D66F
|#3 0x51B70B in ecrspe_
|#4 0x501C54 in wac_
|#5 0x43C596 in telemac3d_
|#6 0x407705 in MAIN__ at homere_telemac3d.f:?
|~~~~~~~~~~~~~~~~~~

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TOPIC: step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel

step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25217

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step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25219

step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25285

step-by-step : install Telemac [v7p2-v7p1] Ubuntu 16.04 in parallel 7 years 9 months ago #25294

step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 9 months ago #25354

step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 9 months ago #25359

step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25394

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step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25396

step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25416

step-by-step guide to install Telemac v7p1 on Ubuntu 16.04 in parallel 7 years 8 months ago #25533

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