Compiling Delft3D on 64 bit Linux - D-Flow Flexible Mesh - Delft3D
intro story D-Flow FM
D-Flow Flexible MeshD-Flow Flexible Mesh (D-Flow FM) is the new software engine for hydrodynamical simulations on unstructured grids in 1D-2D-3D. Together with the familiar curvilinear meshes from Delft3D 4, the unstructured grid can consist of triangles, pentagons (etc.) and 1D channel networks, all in one single mesh. It combines proven technology from the hydrodynamic engines of Delft3D 4 and SOBEK 2 and adds flexible administration, resulting in:
An overview of the current developments can be found here. The D-Flow FM - team would be delighted if you would participate in discussions on the generation of meshes, the specification of boundary conditions, the running of computations, and all kinds of other relevant topics. Feel free to share your smart questions and/or brilliant solutions!
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Compiling Delft3D on 64 bit Linux
BZ
Barbara Zemskova, modified 9 Years ago.
Compiling Delft3D on 64 bit Linux
Youngling Posts: 5 Join Date: 8/31/11 Recent Posts 00
Hello,
We are trying to install Delft3D on our new 64 bit Linux cluster. Our system administrator was able to get the source code to compile, but encountered the following error when trying to run one of the examples:
../../src/bin/deltares_hydro.exe: symbol lookup error: ../../src/lib/libflow2d3d.so: undefined symbol: small_
They thought the issue was related to the X11 development tools, which they installed, but it did not fix the error.
Any suggestions would be greatly appreciated.
--Brian
We are trying to install Delft3D on our new 64 bit Linux cluster. Our system administrator was able to get the source code to compile, but encountered the following error when trying to run one of the examples:
../../src/bin/deltares_hydro.exe: symbol lookup error: ../../src/lib/libflow2d3d.so: undefined symbol: small_
They thought the issue was related to the X11 development tools, which they installed, but it did not fix the error.
Any suggestions would be greatly appreciated.
--Brian
Adri Mourits, modified 9 Years ago.
RE: Compiling Delft3D on 64 bit Linux
Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts 00
Hi Brian/Barbara,
"small" is a tiny little subroutine in subdirectory "src\utils_lgpl\utils_flow\packages\utils_flow\src". When compiling/linking, it should be packed inside libflow2d3d.so. Can you post your "logs/make.log" file? May be that gives more information.
Thanks.
Regards,
Adri
"small" is a tiny little subroutine in subdirectory "src\utils_lgpl\utils_flow\packages\utils_flow\src". When compiling/linking, it should be packed inside libflow2d3d.so. Can you post your "logs/make.log" file? May be that gives more information.
Thanks.
Regards,
Adri
BZ
Barbara Zemskova, modified 9 Years ago.
RE: Compiling Delft3D on 64 bit Linux
Youngling Posts: 5 Join Date: 8/31/11 Recent Posts 00
Hi Adri,
Thanks for your response. Here is a copy of the log file you requested.
Thanks again!
Thanks for your response. Here is a copy of the log file you requested.
Thanks again!
Attachments:
Adri Mourits, modified 9 Years ago.
RE: Compiling Delft3D on 64 bit Linux
Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts 00
Hi,
I see nothing strange up to the error message.
Does file "/netscr/shubin/test/Brian_White/delft3d_repository/src/utils_lgpl/utils_flow/packages/utils_flow_c/src/libutils_flow_c.a" exist?
Does file "/netscr/shubin/test/Brian_White/delft3d_repository/src/lib/libutils_flow_c.a" exist?
Did an additional error message appear on the screen when running "build.sh"?
There is something I don't understand. This make.log file suggests that you did not succeed in building libflow2d3d.so. But in your previous post, the error message was "symbol lookup error: ../../src/lib/libflow2d3d.so: undefined symbol: small_"
which suggests that you DO have a libflow2d3d.so. Did you start the calculation using a newly build libflow2d3d.so?
Regards,
Adri
I see nothing strange up to the error message.
Does file "/netscr/shubin/test/Brian_White/delft3d_repository/src/utils_lgpl/utils_flow/packages/utils_flow_c/src/libutils_flow_c.a" exist?
Does file "/netscr/shubin/test/Brian_White/delft3d_repository/src/lib/libutils_flow_c.a" exist?
Did an additional error message appear on the screen when running "build.sh"?
There is something I don't understand. This make.log file suggests that you did not succeed in building libflow2d3d.so. But in your previous post, the error message was "symbol lookup error: ../../src/lib/libflow2d3d.so: undefined symbol: small_"
which suggests that you DO have a libflow2d3d.so. Did you start the calculation using a newly build libflow2d3d.so?
Regards,
Adri
Hello Adri,
I am trying to compile tagged version 5.00.07.1698 on my Linux (Ubuntu 11.10) 64bit machine.
'autogen.sh' and 'configure.sh' runs fine. However, I get 'make fails' message with following error.
I have also attached all three LOG files.
It seems like the error is related to 'third_party_open' model openDA.
I was successful in installing required mpich2 version with intel compilers on my computer; therefore, I am using intel fortran compiler (latest non-commercial) to build delft3d.
Please suggest me in this regard.
ERROR MESSAGES:
libtool: compile: ifort -I../../../../../utils_lgpl/precision/include -I../../../../../utils_lgpl/esmfsm/include -I../../../../../third_party_open/openda/core/native/include -I../../../../../utils_lgpl/precision/packages/precision/src -I../../../../../utils_lgpl/ec_module/packages/ec_module/src -I../../../../../utils_lgpl/inifiles/packages/inifiles/src -I../../../../../utils_lgpl/meteo/packages/meteo/src -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I../../../../../engines_gpl/flow2d3d/packages/data/src/gdp -I../../../../../engines_gpl/flow2d3d/packages/data/src/basics -I../../../../../engines_gpl/flow2d3d/packages/manager/src -I../../../../../engines_gpl/flow2d3d/packages/kernel/src/inichk -DWITH_DELFTONLINE -O2 -fPIC -m64 -fopenmp -fpp -recursive -reentrancy threaded -traceback -c flow2d3d_f.f90 -fPIC -o .libs/flow2d3d_f.o
flow2d3d_f.f90(39): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [D3D_OLV_CLASS]
use m_openda_olv
--------^
flow2d3d_f.f90(99): error #6404: This name does not have a type, and must have an explicit type. [OPENDA_OLV_HANDLE]
retval = trisim_init(numdom, nummap, context_id, fsm_flags, runID, openda_olv_handle, gdp)
-----------------------------------------------------------------------^
flow2d3d_f.f90(197): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [D3D_OLV_CLASS]
use m_openda_olv
--------^
flow2d3d_f.f90(224): error #6404: This name does not have a type, and must have an explicit type. [OPENDA_OLV_HANDLE]
retVal = trisim_step(openda_olv_handle, gdp)
-------------------------^
flow2d3d_f.f90(236): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [D3D_OLV_CLASS]
use m_openda_olv
--------^
flow2d3d_f.f90(249): error #6404: This name does not have a type, and must have an explicit type. [OPENDA_OLV_HANDLE]
retval = trisim_finish(openda_olv_handle, gdp)
---------------------------^
compilation aborted for flow2d3d_f.f90 (code 1)
make[6]: *** [flow2d3d_f.lo] Error 1
make[6]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/flow2d3d_openda/src'
make[5]: *** [install] Error 2
make[5]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/flow2d3d_openda/src'
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/flow2d3d_openda'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl'
make: *** [install-recursive] Error 1
I am trying to compile tagged version 5.00.07.1698 on my Linux (Ubuntu 11.10) 64bit machine.
'autogen.sh' and 'configure.sh' runs fine. However, I get 'make fails' message with following error.
I have also attached all three LOG files.
It seems like the error is related to 'third_party_open' model openDA.
I was successful in installing required mpich2 version with intel compilers on my computer; therefore, I am using intel fortran compiler (latest non-commercial) to build delft3d.
Please suggest me in this regard.
ERROR MESSAGES:
libtool: compile: ifort -I../../../../../utils_lgpl/precision/include -I../../../../../utils_lgpl/esmfsm/include -I../../../../../third_party_open/openda/core/native/include -I../../../../../utils_lgpl/precision/packages/precision/src -I../../../../../utils_lgpl/ec_module/packages/ec_module/src -I../../../../../utils_lgpl/inifiles/packages/inifiles/src -I../../../../../utils_lgpl/meteo/packages/meteo/src -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I../../../../../engines_gpl/flow2d3d/packages/data/src/gdp -I../../../../../engines_gpl/flow2d3d/packages/data/src/basics -I../../../../../engines_gpl/flow2d3d/packages/manager/src -I../../../../../engines_gpl/flow2d3d/packages/kernel/src/inichk -DWITH_DELFTONLINE -O2 -fPIC -m64 -fopenmp -fpp -recursive -reentrancy threaded -traceback -c flow2d3d_f.f90 -fPIC -o .libs/flow2d3d_f.o
flow2d3d_f.f90(39): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [D3D_OLV_CLASS]
use m_openda_olv
--------^
flow2d3d_f.f90(99): error #6404: This name does not have a type, and must have an explicit type. [OPENDA_OLV_HANDLE]
retval = trisim_init(numdom, nummap, context_id, fsm_flags, runID, openda_olv_handle, gdp)
-----------------------------------------------------------------------^
flow2d3d_f.f90(197): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [D3D_OLV_CLASS]
use m_openda_olv
--------^
flow2d3d_f.f90(224): error #6404: This name does not have a type, and must have an explicit type. [OPENDA_OLV_HANDLE]
retVal = trisim_step(openda_olv_handle, gdp)
-------------------------^
flow2d3d_f.f90(236): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [D3D_OLV_CLASS]
use m_openda_olv
--------^
flow2d3d_f.f90(249): error #6404: This name does not have a type, and must have an explicit type. [OPENDA_OLV_HANDLE]
retval = trisim_finish(openda_olv_handle, gdp)
---------------------------^
compilation aborted for flow2d3d_f.f90 (code 1)
make[6]: *** [flow2d3d_f.lo] Error 1
make[6]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/flow2d3d_openda/src'
make[5]: *** [install] Error 2
make[5]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/flow2d3d_openda/src'
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/flow2d3d_openda'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/abhishek/Downloads/delft_repository/src/engines_gpl'
make: *** [install-recursive] Error 1
Attachments:
Adri Mourits, modified 8 Years ago.
RE: Compiling Delft3D on 64 bit Linux
Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts 00
Hi Abhishek Sharma,
I don't understand what is going wrong. According to your make.log, file "d3d_in_openda.f90" is compiled without problems. This should have generated the needed mod-file. The following file should be present on your system:
/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/kernel/src/inichk/m_openda_olv.mod
Can you check that?
The good news is that you did manage to build libflow2d3d.so. As a workaround, you can skip the compilation of flow2d3d_openda as follows:
Open the following file in a text editor:
/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/Makefile.am
Replace the last two lines:
flow2d3d \
flow2d3d_openda
By
flow2d3d
Don't forget to remove the backslash at the end of the one-but-last line. The file must contain an empty line at the end.
Regards,
Adri
I don't understand what is going wrong. According to your make.log, file "d3d_in_openda.f90" is compiled without problems. This should have generated the needed mod-file. The following file should be present on your system:
/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/kernel/src/inichk/m_openda_olv.mod
Can you check that?
The good news is that you did manage to build libflow2d3d.so. As a workaround, you can skip the compilation of flow2d3d_openda as follows:
Open the following file in a text editor:
/home/abhishek/Downloads/delft_repository/src/engines_gpl/flow2d3d/packages/Makefile.am
Replace the last two lines:
flow2d3d \
flow2d3d_openda
By
flow2d3d
Don't forget to remove the backslash at the end of the one-but-last line. The file must contain an empty line at the end.
Regards,
Adri