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error compiling TOUGH3 on Ubuntu : Failed to build TOUGH TPLS

CMakeError.log

Hi All,

I tried to compile TOUGH3 on a new server with Ubuntu 20.04 but not successful. (Please refer to the error.png for error screenshot).

I have all dependencies installed and their versions look like below:

cmake 3.16.3

gcc 9.4.0

mpirun 4.0.3

I tried solutions below in the user forum with the same error (change the PETSC_VERSION_PATCH to 4, and add the BLAS version 3.5.0) but they did not work for me.

https://tough.forumbee.com/t/36w3x7/compiling-tough3-on-linux-platform-ubuntu

https://tough.forumbee.com/t/h44nsl/compiling-tough3-on-linux-platform-ubuntu-failed-to-configure-tough-tpls

I attached the cmakerror file for your reference. Can anyone help me out?

Thanks in advance,

 

Haiyan

49 replies

null
      • kenny
      • 1 yr agoFri, June 30, 2023 at 10:53 PM UTC
      • Reported - view

      This is a petsc installation problem. This problem was also reported by another user.  Why do not you try reliable (a little older) version, such as Ver 3.18.x 

        • Yessica_Peralta
        • 1 yr agoMon, July 10, 2023 at 9:03 PM UTC
        • Reported - view

        kenny Hi Kenny, I could install Petsc, now I am having the following error:

        [ 52%] Building Fortran object src/CMakeFiles/tough3-eco2n.dir/zevsreale.f90.o
        cd /home/yplinux/tough3-build/esd-tough3/build/tough-build-eco2n/src && /usr/local/bin/mpif90 -DTF_ECO2N_V1 -DUSE_MPI -DUSE_PETSC -I/home/yplinux/tough3-build/esd-tough3/src -I/home/yplinux/tough3-build/esd-tough3/tough3-install/tpls/include  -fallow-argument-mismatch   -c /home/yplinux/tough3-build/esd-tough3/src/zevsreale.f90 -o CMakeFiles/tough3-eco2n.dir/zevsreale.f90.o
        /home/yplinux/tough3-build/esd-tough3/src/zevsreale.f90:1551:100:

         1551 |          DO 10 J=1,NumCom
              |                                                                                                    1
        Warning: Fortran 2018 deleted feature: Shared DO termination label 10 at (1)
        /home/yplinux/tough3-build/esd-tough3/src/zevsreale.f90:1392:31:

         1392 |       if(tempC.gt.100.d0) pref=func(p_coe(1),p_coe(2),p_coe(3),p_coe(4),p_coe(5),tempC)
              |                               1
        Error: Type mismatch in argument ‘a’ at (1); passed REAL(4) to REAL(8)
        /home/yplinux/tough3-build/esd-tough3/src/zevsreale.f90:1410:8:

         1410 |      &  func(coef(1,ns),coef(2,ns),coef(3,ns)         &
              |        1
        Error: Type mismatch in argument ‘a’ at (1); passed REAL(4) to REAL(8)
        /home/yplinux/tough3-build/esd-tough3/src/zevsreale.f90:1425:22:

         1425 |          alogK(nco2)= func(cco2L(1),cco2L(2),cco2L(3),cco2L(4),cco2L(5),tempC)
              |                      1
        Error: Type mismatch in argument ‘a’ at (1); passed REAL(4) to REAL(8)
        /home/yplinux/tough3-build/esd-tough3/src/zevsreale.f90:1429:21:

         1429 |          alogK(nco2)=func(cco2(1),cco2(2),cco2(3),cco2(4),cco2(5),tempC)
              |                     1
        Error: Type mismatch in argument ‘a’ at (1); passed REAL(4) to REAL(8)
        make[2]: *** [src/CMakeFiles/tough3-eco2n.dir/build.make:378: src/CMakeFiles/tough3-eco2n.dir/zevsreale.f90.o] Error 1
        make[2]: Leaving directory '/home/yplinux/tough3-build/esd-tough3/build/tough-build-eco2n'
        make[1]: *** [CMakeFiles/Makefile2:90: src/CMakeFiles/tough3-eco2n.dir/all] Error 2
        make[1]: Leaving directory '/home/yplinux/tough3-build/esd-tough3/build/tough-build-eco2n'
        make: *** [Makefile:144: all] Error 2
        Script ERROR: Failed to build TOUGH

        • Yessica_Peralta
        • 1 yr agoMon, July 10, 2023 at 9:05 PM UTC
        • Reported - view

        Yessica Peralta I copied and pasted the paragraph you suggested on the CMakefiles. It looks like worked for most of the things however at the end is having this error. Have you seen it before? 

        • Yessica_Peralta
        • 1 yr agoMon, July 10, 2023 at 9:14 PM UTC
        • Reported - view

        kenny I copied and pasted the paragraph you suggested on the CMakefiles. It looks like worked for most of the things however at the end is having this error. Have you seen it before? 

        • Yogendra_Narayanan_Sures
        • 1 yr agoThu, March 14, 2024 at 12:34 PM UTC
        • Reported - view

          , Can you please help me in overcoming the above error. I modified the CMake Lists in both the locations. I have attached the Cmake file for your reference. Thank you in advance.

        Cmake tough3.txt Cmake toughlibsrc.txt
        • Yessica_Peralta
        • 1 yr agoThu, March 14, 2024 at 3:49 PM UTC
        • Reported - view

         I think you need to recompile PETSC and test it. Please, read the previous steps in this post, that was what I did. 

        • Yogendra_Narayanan_Sures
        • 1 yr agoFri, March 15, 2024 at 10:05 AM UTC
        • Reported - view

         I have recompiled but same error is persisting...I have modified the Cmake files for gfortran also which I have attached earlier. 

        • Yessica_Peralta
        • 1 yr agoMon, March 18, 2024 at 3:37 PM UTC
        • Reported - view

        Did you test the PETSC installation?. To make sure that your PETSC is installed correctly. Here is the website of the LBNL https://marketplace.lbl.gov/tough/. I think Kenny referred it in his previous replied to update the TOUGH3 V1.1

        • Yogendra_Narayanan_Sures
        • 1 yr agoMon, March 18, 2024 at 5:39 PM UTC
        • Reported - view

         Thank you for sharing the link. Since, we already have version TOUGH3 1.0, it was mentioned that version TOUGH3 V1.1 will be free of cost to upgrade. Could you tell me the procedure to get it upgraded. Thanks in advance.

        • Yessica_Peralta
        • 1 yr agoMon, March 18, 2024 at 6:12 PM UTC
        • Reported - view

         I think you can email Yingqi YQZhang@lbl.gov or Kenny too. Yingqi gave me the updated version last time. 

        • Yogendra_Narayanan_Sures
        • 1 yr agoMon, March 25, 2024 at 11:42 AM UTC
        • Reported - view

         Thank you. I have got the version 1.1

      • Yessica_Peralta
      • 1 yr agoFri, June 30, 2023 at 10:56 PM UTC
      • Reported - view

      I will

      • kenny
      • 1 yr agoMon, July 10, 2023 at 11:57 PM UTC
      • Reported - view

      This is the still the same error (data type dismatch) . Are you sure you have correctly fixed the cmake scripts  by adding "-fallow-argument-mismatch" in 

      1. esd-tough3/CMakeLists.txt (which is the code snippet you showed me), and
      2. esd-toughlib/src/CMakeLists.txt.
      • Yessica_Peralta
      • 1 yr agoTue, July 11, 2023 at 4:48 PM UTC
      • Reported - view

      Here is the esd-toughlib/src/CMakeLists.txt with the "-fallow-argument-mismatch" in. Maybe the if and endif are well aligned?. what do you think?

      CMakeLists.txt
      • Yessica_Peralta
      • 1 yr agoTue, July 11, 2023 at 4:59 PM UTC
      • Reported - view

      Here are the ones. esd-tough3/CMakeLists.txt and esd-toughlib/src/CMakeLists.txt. Please discard the one I sent before

      CMakeLists.txt CMakeLists.txt
      • kenny
      • 1 yr agoTue, July 11, 2023 at 5:03 PM UTC
      • Reported - view

      The attached one looks good. The problem appeared during zevsreale.f90 compilation, which is compiled with the CMakeLists.txt in esd-tough3/. Have you fixed it?

      • Yessica_Peralta
      • 1 yr agoTue, July 11, 2023 at 5:21 PM UTC
      • Reported - view

      I think so. This is the one in esd-tough3/src 

      CMakeLists.txt
      • Yessica_Peralta
      • 1 yr agoTue, July 11, 2023 at 5:23 PM UTC
      • Reported - view

      so I fixed both the one that is inside the src in both esd-tough3 and the one that is in esd-tough3

      • Yessica_Peralta
      • 1 yr agoTue, July 11, 2023 at 5:27 PM UTC
      • Reported - view

      This is the error log

      CMakeError.log
      • kenny
      • 1 yr agoTue, July 11, 2023 at 5:35 PM UTC
      • Reported - view

      Seems you did not do it correctly for fixing the cmake script. The "-fallow-argument-mismatch" must apply to "GNU" compiler, not "Intel".  I am attaching the correct one. Use this one to replace the one at esd-toughlib/src/CMakeLists.txt. You need delete 'Build' folder before every recompilation 

      CMakeLists.txt
        • Yessica_Peralta
        • 1 yr agoTue, July 11, 2023 at 6:23 PM UTC
        • Reported - view

        kenny seems like is configure completed. Thank you so much

        • Yessica_Peralta
        • 1 yr agoTue, July 11, 2023 at 8:55 PM UTC
        • Reported - view

        kenny I am trying to run a parallel with 2 or 4 processors with the mpiexec -n 2 and the following message appears: 

        WARNING: Linux kernel CMA support was requested via the
        btl_vader_single_copy_mechanism MCA variable, but CMA support is
        not available due to restrictive ptrace settings.

        The vader shared memory BTL will fall back on another single-copy
        mechanism if one is available. This may result in lower performance

        • Yessica_Peralta
        • 1 yr agoTue, July 11, 2023 at 9:42 PM UTC
        • Reported - view

        Yessica Peralta I fix it with:  

        $ sudo vim /etc/sysctl.d/10-ptrace.conf

        Edit from 1 to 0 

        kernel.yama.ptrace_scope = 0
      • Yessica_Peralta
      • 1 yr agoTue, July 11, 2023 at 8:56 PM UTC
      • Reported - view

      tells me and it is just running with 1 processor, have you seen this message before?

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