New GINA Version

Mailing List Archives ogs-users
1

Dear OGS user and developer. A new GINA Version is on the WebSVN

https://svn.ufz.de/svn/ogs/branches/GINA_OGS

if you have no access to the WebSVN you can download the program from this link:

https://teambeam.bgr.de/my/?m=drive#!folder-68

best regards

2

Dear All,

We announce a new version:

OpenGeoSys 5.5.4 (WW/NW/LB) - 27.06.2014
The version includes
1 Rewritten member functions of class matrix_class that gives better performance in the local assembly computation. With the changes, the computation time for the problem using large local matrix (e.g deformation problems) becomes shorter than the previous versions.
2 Parallel binary I/O for parallel computing with PETSc. With the changes, partmesh outputs binary files by default if option '-asci' is not used. (How to use this binary IO, please refer to the updated page: https://svn.ufz.de/ogs/wiki/PETScPage)
3 Parallelization of the pressure saturation scheme (PS_GLOBAL) with PETSc, and a new benchmark for which is added.
4 OGS_FEM_BRNS now requires BLAS and LAPACK libraries during compilation under UNIX
5 Added MKL_DIR option in CMake to specify a root dir of MKL.
6 Reactivated benchmkars configured for OGS_FEM_LIS and OGS_FEM_MKL.
7 Some other bug fixings in point search on surfaces, PS_GLOBAL, VTK output, FEFLOW import, etc

This is also a first attempt to maintain OGS5 development by using github (https://github.com/envinf/ogs5-trunk/issues/3#issuecomment-42513384). With this way, changes in the source code are committed to forks of OGS5 github repository (https://github.com/envinf/ogs5-trunk.git), reviewed for merging (important but it was missing before), merged to OGS5 github repository and finally committed to the svn repository. Thanks Nori and Lars for transplanting the svn repository to the git repository.

Wenqing, Norihiro, Lars

3

WOW, this version sounds very integrated with several killing features that I should keep an eye on. Great job, guys. Keep up the good work.

···

Chan-Hee

On Fri, Jun 27, 2014 at 9:59 PM, Wenqing Wang wenqing.wang@ufz.de wrote:

Dear All,

We announce a new version:

OpenGeoSys 5.5.4 (WW/NW/LB) - 27.06.2014

The version includes

1 Rewritten member functions of class matrix_class that gives better performance in the local assembly computation. With the changes, the computation time for the problem using large local matrix (e.g deformation problems) becomes shorter than the previous versions.

2 Parallel binary I/O for parallel computing with PETSc. With the changes, partmesh outputs binary files by default if option ‘-asci’ is not used. (How to use this binary IO, please refer to the updated page: https://svn.ufz.de/ogs/wiki/PETScPage)

3 Parallelization of the pressure saturation scheme (PS_GLOBAL) with PETSc, and a new benchmark for which is added.

4 OGS_FEM_BRNS now requires BLAS and LAPACK libraries during compilation under UNIX

5 Added MKL_DIR option in CMake to specify a root dir of MKL.

6 Reactivated benchmkars configured for OGS_FEM_LIS and OGS_FEM_MKL.

7 Some other bug fixings in point search on surfaces, PS_GLOBAL, VTK output, FEFLOW import, etc

This is also a first attempt to maintain OGS5 development by using github (https://github.com/envinf/ogs5-trunk/issues/3#issuecomment-42513384). With this way, changes in the source code are committed to forks of OGS5 github repository (https://github.com/envinf/ogs5-trunk.git), reviewed for merging (important but it was missing before), merged to OGS5 github repository and finally committed to the svn repository. Thanks Nori and Lars for transplanting the svn repository to the git repository.

Wenqing, Norihiro, Lars

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4

Hi all,
I tried to extract a fresh copy of OGS5 on the cray ...It worked a while
ago, but with svn I get now the following error:

svn co georg/SOFT> svn co https://svn.ufz.de/svn/ogs/trunk
svn: OPTIONS of 'https://svn.ufz.de/svn/ogs/trunk': SSL negotiation
failed: SSL error: unexpected message (https://svn.ufz.de)

Does someone have an idea if this is related to the server side or maybe
to the client side?

Then I got the idea to use the "new" git repository for ogs5:

georg/SOFT> git clone https://github.com/envinf/ogs5-trunk.git sources
Cloning into 'sources'...
error: error:0D0C50A1:asn1 encoding routines:ASN1_item_verify:unknown
message digest algorithm while accessing
https://github.com/envinf/ogs5-trunk.git/info/refs
fatal: HTTP request failed

and next try replacing https with git:
georg/SOFT> git clone git://github.com/envinf/ogs5-trunk.git sources
Cloning into 'sources'...
fatal: remote error:
  Repository not found.

Any idea what I have to do? Is the repository private and not for public
or member access?
Only for your information, git works, as I get ogs6:

georg/SOFT> git clone git://github.com/ufz/ogs.git sources
Cloning into 'sources'...
remote: Reusing existing pack: 25064, done.
remote: Total 25064 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (25064/25064), 6.15 MiB | 1.65 MiB/s, done.
Resolving deltas: 100% (18386/18386), done.

thanks, Georg

···

On 06/27/2014 02:59 PM, Wenqing Wang wrote:

Dear All,

We announce a new version:

OpenGeoSys 5.5.4 (WW/NW/LB) - 27.06.2014
The version includes
1 Rewritten member functions of class matrix_class that gives
better performance in the local assembly computation. With the
changes, the computation time for the problem using large local matrix
(e.g deformation problems) becomes shorter than the previous versions.
2 Parallel binary I/O for parallel computing with PETSc. With the
changes, partmesh outputs binary files by default if option '-asci' is
not used. (How to use this binary IO, please refer to the updated
page: https://svn.ufz.de/ogs/wiki/PETScPage\)
3 Parallelization of the pressure saturation scheme (PS_GLOBAL)
with PETSc, and a new benchmark for which is added.
4 OGS_FEM_BRNS now requires BLAS and LAPACK libraries during
compilation under UNIX
5 Added MKL_DIR option in CMake to specify a root dir of MKL.
6 Reactivated benchmkars configured for OGS_FEM_LIS and OGS_FEM_MKL.
7 Some other bug fixings in point search on surfaces, PS_GLOBAL,
VTK output, FEFLOW import, etc

This is also a first attempt to maintain OGS5 development by using
github
(https://github.com/envinf/ogs5-trunk/issues/3#issuecomment-42513384\).
With this way, changes in the source code are committed to forks of
OGS5 github repository (https://github.com/envinf/ogs5-trunk.git\),
reviewed for merging (important but it was missing before), merged to
OGS5 github repository and finally committed to the svn repository.
Thanks Nori and Lars for transplanting the svn repository to the git
repository.

Wenqing, Norihiro, Lars

--
PD Dr. Georg Kosakowski * Laboratory for Waste Management
Paul Scherrer Institut * 5232 Villigen/PSI * Switzerland
Phone: +41-56-3104743 * Email: georg.kosakowski@psi.ch
homepage: Georg Kosakowski | LES | Paul Scherrer Institut (PSI)

5

Hi Georg,

If I remember it correctly, a SSH key of the server was changed some time ago when a critical security issue was found in OpenSSL library. You may need to reset SSH setting to connect the server.

The repository on GitHub is private one and only our department members cab access it at the moment.

Best,
Nori

···

On 07/02/2014 10:19 AM, Georg Kosakowski wrote:

Hi all,
I tried to extract a fresh copy of OGS5 on the cray ...It worked a while
ago, but with svn I get now the following error:

svn co georg/SOFT> svn co https://svn.ufz.de/svn/ogs/trunk
svn: OPTIONS of 'https://svn.ufz.de/svn/ogs/trunk': SSL negotiation
failed: SSL error: unexpected message (https://svn.ufz.de)

Does someone have an idea if this is related to the server side or maybe
to the client side?

Then I got the idea to use the "new" git repository for ogs5:

georg/SOFT> git clone https://github.com/envinf/ogs5-trunk.git sources
Cloning into 'sources'...
error: error:0D0C50A1:asn1 encoding routines:ASN1_item_verify:unknown
message digest algorithm while accessing
https://github.com/envinf/ogs5-trunk.git/info/refs
fatal: HTTP request failed

and next try replacing https with git:
georg/SOFT> git clone git://github.com/envinf/ogs5-trunk.git sources
Cloning into 'sources'...
fatal: remote error:
   Repository not found.

Any idea what I have to do? Is the repository private and not for public
or member access?
Only for your information, git works, as I get ogs6:

georg/SOFT> git clone git://github.com/ufz/ogs.git sources
Cloning into 'sources'...
remote: Reusing existing pack: 25064, done.
remote: Total 25064 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (25064/25064), 6.15 MiB | 1.65 MiB/s, done.
Resolving deltas: 100% (18386/18386), done.

thanks, Georg

On 06/27/2014 02:59 PM, Wenqing Wang wrote:

Dear All,

We announce a new version:

OpenGeoSys 5.5.4 (WW/NW/LB) - 27.06.2014
The version includes
1 Rewritten member functions of class matrix_class that gives
better performance in the local assembly computation. With the
changes, the computation time for the problem using large local matrix
(e.g deformation problems) becomes shorter than the previous versions.
2 Parallel binary I/O for parallel computing with PETSc. With the
changes, partmesh outputs binary files by default if option '-asci' is
not used. (How to use this binary IO, please refer to the updated
page: https://svn.ufz.de/ogs/wiki/PETScPage\)
3 Parallelization of the pressure saturation scheme (PS_GLOBAL)
with PETSc, and a new benchmark for which is added.
4 OGS_FEM_BRNS now requires BLAS and LAPACK libraries during
compilation under UNIX
5 Added MKL_DIR option in CMake to specify a root dir of MKL.
6 Reactivated benchmkars configured for OGS_FEM_LIS and OGS_FEM_MKL.
7 Some other bug fixings in point search on surfaces, PS_GLOBAL,
VTK output, FEFLOW import, etc

This is also a first attempt to maintain OGS5 development by using
github
(https://github.com/envinf/ogs5-trunk/issues/3#issuecomment-42513384\).
With this way, changes in the source code are committed to forks of
OGS5 github repository (https://github.com/envinf/ogs5-trunk.git\),
reviewed for merging (important but it was missing before), merged to
OGS5 github repository and finally committed to the svn repository.
Thanks Nori and Lars for transplanting the svn repository to the git
repository.

Wenqing, Norihiro, Lars

--
Norihiro Watanabe, Dr.-Ing.
Department of Environmental Informatics (ENVINF)
Wissenschaftler

Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15 / 04318 Leipzig / Germany

norihiro.watanabe@ufz.de / http://www.ufz.de
Telefon +49 341 235 1806

Sitz der Gesellschaft: Leipzig
Registergericht: Amtsgericht Leipzig, Handelsregister Nr. B 4703
Vorsitzender des Aufsichtsrats: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer: Prof. Dr. Georg Teutsch
Administrativer Geschäftsführer: Dr. Heike Graßmann

6

Hi,
finally I managed to find a workaround for one of the access methods.
On the cray git is linked to a "very old" OpenSSL version. In order to
access the git repository via https one can do this under linux:

env GIT_SSL_NO_VERIFY=true git clone
https://github.com/envinf/ogs5-trunk.git ogs5

Greetings, Georg

···

On 07/02/2014 11:22 AM, Norihiro Watanabe wrote:

Hi Georg,

If I remember it correctly, a SSH key of the server was changed some
time ago when a critical security issue was found in OpenSSL library.
You may need to reset SSH setting to connect the server.

The repository on GitHub is private one and only our department
members cab access it at the moment.

Best,
Nori

On 07/02/2014 10:19 AM, Georg Kosakowski wrote:

Hi all,
I tried to extract a fresh copy of OGS5 on the cray ...It worked a while
ago, but with svn I get now the following error:

svn co georg/SOFT> svn co https://svn.ufz.de/svn/ogs/trunk
svn: OPTIONS of 'https://svn.ufz.de/svn/ogs/trunk': SSL negotiation
failed: SSL error: unexpected message (https://svn.ufz.de)

Does someone have an idea if this is related to the server side or maybe
to the client side?

Then I got the idea to use the "new" git repository for ogs5:

georg/SOFT> git clone https://github.com/envinf/ogs5-trunk.git sources
Cloning into 'sources'...
error: error:0D0C50A1:asn1 encoding routines:ASN1_item_verify:unknown
message digest algorithm while accessing
https://github.com/envinf/ogs5-trunk.git/info/refs
fatal: HTTP request failed

and next try replacing https with git:
georg/SOFT> git clone git://github.com/envinf/ogs5-trunk.git sources
Cloning into 'sources'...
fatal: remote error:
   Repository not found.

Any idea what I have to do? Is the repository private and not for public
or member access?
Only for your information, git works, as I get ogs6:

georg/SOFT> git clone git://github.com/ufz/ogs.git sources
Cloning into 'sources'...
remote: Reusing existing pack: 25064, done.
remote: Total 25064 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (25064/25064), 6.15 MiB | 1.65 MiB/s, done.
Resolving deltas: 100% (18386/18386), done.

thanks, Georg

On 06/27/2014 02:59 PM, Wenqing Wang wrote:

Dear All,

We announce a new version:

OpenGeoSys 5.5.4 (WW/NW/LB) - 27.06.2014
The version includes
1 Rewritten member functions of class matrix_class that gives
better performance in the local assembly computation. With the
changes, the computation time for the problem using large local matrix
(e.g deformation problems) becomes shorter than the previous versions.
2 Parallel binary I/O for parallel computing with PETSc. With the
changes, partmesh outputs binary files by default if option '-asci' is
not used. (How to use this binary IO, please refer to the updated
page: https://svn.ufz.de/ogs/wiki/PETScPage\)
3 Parallelization of the pressure saturation scheme (PS_GLOBAL)
with PETSc, and a new benchmark for which is added.
4 OGS_FEM_BRNS now requires BLAS and LAPACK libraries during
compilation under UNIX
5 Added MKL_DIR option in CMake to specify a root dir of MKL.
6 Reactivated benchmkars configured for OGS_FEM_LIS and OGS_FEM_MKL.
7 Some other bug fixings in point search on surfaces, PS_GLOBAL,
VTK output, FEFLOW import, etc

This is also a first attempt to maintain OGS5 development by using
github
(https://github.com/envinf/ogs5-trunk/issues/3#issuecomment-42513384\).
With this way, changes in the source code are committed to forks of
OGS5 github repository (https://github.com/envinf/ogs5-trunk.git\),
reviewed for merging (important but it was missing before), merged to
OGS5 github repository and finally committed to the svn repository.
Thanks Nori and Lars for transplanting the svn repository to the git
repository.

Wenqing, Norihiro, Lars

--
PD Dr. Georg Kosakowski * Laboratory for Waste Management
Paul Scherrer Institut * 5232 Villigen/PSI * Switzerland
Phone: +41-56-3104743 * Email: georg.kosakowski@psi.ch
homepage: Georg Kosakowski | LES | Paul Scherrer Institut (PSI)

7

Thanks Nori. I noticed your change made in FindMKL.cmake some weeks ago. Better than the previous. With that change considered, I could compile OGS 5.5.4 with MKL using intel C++ compiler no problem. The compilation option that I used is following. Just for the tips who may be interested.

cmake /home/nbeyond/svn/ogs/trunk/sources -DOGS_FEM_MKL=ON -DPARALLEL_USE_OPENMP=ON -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DMKL_DIR=/opt/intel/mkl

Note that MKL_DIR should be your MKL root directory. Other than that, I think it’s pretty straight forward. Once again, with multiphase flow module and MKL simultaneously live, I am on OGS 5.5.4.

Cheers,

···

Chan-Hee Park, Ph.D.

Phone: +82 42 868 3502
Fax: +82 42 868 3358

Geothermal Resources Team
Korea Institute of Geoscience and Mineral Resources (KIGAM)

124 Gwahang-no, Yuseong-gu, Daejeon 305-350, KOREA

On Thu, Jul 3, 2014 at 3:36 PM, Georg Kosakowski georg.kosakowski@psi.ch wrote:

Hi,

finally I managed to find a workaround for one of the access methods.

On the cray git is linked to a “very old” OpenSSL version. In order to

access the git repository via https one can do this under linux:

env GIT_SSL_NO_VERIFY=true git clone

https://github.com/envinf/ogs5-trunk.git ogs5

Greetings, Georg

On 07/02/2014 11:22 AM, Norihiro Watanabe wrote:

Hi Georg,

If I remember it correctly, a SSH key of the server was changed some

time ago when a critical security issue was found in OpenSSL library.

You may need to reset SSH setting to connect the server.

The repository on GitHub is private one and only our department

members cab access it at the moment.

Best,

Nori

On 07/02/2014 10:19 AM, Georg Kosakowski wrote:

Hi all,

I tried to extract a fresh copy of OGS5 on the cray …It worked a while

ago, but with svn I get now the following error:

svn co georg/SOFT> svn co https://svn.ufz.de/svn/ogs/trunk

svn: OPTIONS of ‘https://svn.ufz.de/svn/ogs/trunk’: SSL negotiation

failed: SSL error: unexpected message (https://svn.ufz.de)

Does someone have an idea if this is related to the server side or maybe

to the client side?

Then I got the idea to use the “new” git repository for ogs5:

georg/SOFT> git clone https://github.com/envinf/ogs5-trunk.git sources

Cloning into ‘sources’…

error: error:0D0C50A1:asn1 encoding routines:ASN1_item_verify:unknown

message digest algorithm while accessing

https://github.com/envinf/ogs5-trunk.git/info/refs

fatal: HTTP request failed

and next try replacing https with git:

georg/SOFT> git clone git://github.com/envinf/ogs5-trunk.git sources

Cloning into ‘sources’…

fatal: remote error:

Repository not found.

Any idea what I have to do? Is the repository private and not for public

or member access?

Only for your information, git works, as I get ogs6:

georg/SOFT> git clone git://github.com/ufz/ogs.git sources

Cloning into ‘sources’…

remote: Reusing existing pack: 25064, done.

remote: Total 25064 (delta 0), reused 0 (delta 0)

Receiving objects: 100% (25064/25064), 6.15 MiB | 1.65 MiB/s, done.

Resolving deltas: 100% (18386/18386), done.

thanks, Georg

On 06/27/2014 02:59 PM, Wenqing Wang wrote:

Dear All,

We announce a new version:

OpenGeoSys 5.5.4 (WW/NW/LB) - 27.06.2014

The version includes

1 Rewritten member functions of class matrix_class that gives

better performance in the local assembly computation. With the

changes, the computation time for the problem using large local matrix

(e.g deformation problems) becomes shorter than the previous versions.

2 Parallel binary I/O for parallel computing with PETSc. With the

changes, partmesh outputs binary files by default if option ‘-asci’ is

not used. (How to use this binary IO, please refer to the updated

page: https://svn.ufz.de/ogs/wiki/PETScPage)

3 Parallelization of the pressure saturation scheme (PS_GLOBAL)

with PETSc, and a new benchmark for which is added.

4 OGS_FEM_BRNS now requires BLAS and LAPACK libraries during

compilation under UNIX

5 Added MKL_DIR option in CMake to specify a root dir of MKL.

6 Reactivated benchmkars configured for OGS_FEM_LIS and OGS_FEM_MKL.

7 Some other bug fixings in point search on surfaces, PS_GLOBAL,

VTK output, FEFLOW import, etc

This is also a first attempt to maintain OGS5 development by using

github

(https://github.com/envinf/ogs5-trunk/issues/3#issuecomment-42513384).

With this way, changes in the source code are committed to forks of

OGS5 github repository (https://github.com/envinf/ogs5-trunk.git),

reviewed for merging (important but it was missing before), merged to

OGS5 github repository and finally committed to the svn repository.

Thanks Nori and Lars for transplanting the svn repository to the git

repository.

Wenqing, Norihiro, Lars

–

PD Dr. Georg Kosakowski * Laboratory for Waste Management

Paul Scherrer Institut * 5232 Villigen/PSI * Switzerland

Phone: +41-56-3104743 * Email: georg.kosakowski@psi.ch

homepage: http://www.psi.ch/les/georg-kosakowski

–

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To unsubscribe from this group and stop receiving emails from it, send an email to ogs-users+unsubscribe@googlegroups.com.

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8

Dear GINA_OGS Team,

I am a PhD student at the University of Birmingham please kindly would you help me with the following:

  1. How can I get a tutorial of the GINA as a guide how to apply the THM coupled processes using the GINA only (Not OGS)?

This is very important as long as the with the GINA I can prescribe the Fracture within the HDR geothermal reservoir.

  1. Please, can you provide me with the steps that I need follow to find the distance of the temperature Profile from the injection pressure using OGS? I can find the curves and its temperature in the results but without data (the distance of each curve (0-9) from the injection well).

  2. would you please help me to know how to put different permeability values for a reservoir?

(more than one permeability data input in different length and depth at the same time).

Thank you in advance,

Kind regards,

Maleaha Samin,

PhD student

University of Birmingham

United Kingdom

MYS172@bham.ac.uk

···

On Friday, 27 June 2014 07:06:33 UTC+1, Herbert Kunz wrote:

Dear OGS user and developer. A new GINA Version is on the WebSVN

https://svn.ufz.de/svn/ogs/branches/GINA_OGS

if you have no access to the WebSVN you can download the program from this link:

https://teambeam.bgr.de/my/?m=drive#!folder-68

best regards

Herbert Kunz

Geologisch-geotechnische Erkundung

BGR Bundesanstalt für Geowissenschaften und Rohstoffe

GEOZENTRUM HANNOVER

Stilleweg 2

30 659 Hannover

Tel.: 0511 - 643 2419

www.geozentrum-hannover.de www.bgr.bund.de