cpseis / Bugs / #141 cfe: unable to set Length of traces and DT in JOB

kerim khemraev - 2022-10-05

Downloaded cpseis from trunk 9 october 2022.
And additional picture

Last edit: kerim khemraev 2022-10-05

2022-10-05_03-00-19.jpg

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- Bill Menger - 2022-10-06
  
  This looks like it could be caused by a bad build. My suggestion is to:
  
  $ cd $CPSEIS_INSTALL_DIR/platforms/$CPSEIS_ARCH
  $ make clean;make;make cfe
  $ cd
  $ cd cpsjobs
  $ cfe
  
  If that doesn't fix it, please send the results of:
  echo $CPSEIS_INSTALL_DIR
  echo $CPSEIS_ARCH
  echo $CPSEIS_COMPILER and send a note to bill.menger@gmail.com
  Bill
  
  On 10/5/2022 12:27 PM, kerim khemraev wrote:
  
  Additional picture:
  
  Attachments:
  
  2022-10-05_03-00-19.jpg
  https://sourceforge.net/p/cpseis/bugs/_discuss/thread/28187b3074/8f94/attachment/2022-10-05_03-00-19.jpg
  (154.4 kB; image/jpeg)
  
  [bugs:#141] https://sourceforge.net/p/cpseis/bugs/141/ cfe: unable
  to set Length of traces and DT in JOB_DATA
  
  Status: open
  Group: v1.0 (example)
  Created: Wed Oct 05, 2022 05:26 PM UTC by kerim khemraev
  Last Updated: Wed Oct 05, 2022 05:26 PM UTC
  Owner: nobody
  Attachments:
  
  2022-10-05_03-03-47.jpg
  https://sourceforge.net/p/cpseis/bugs/141/attachment/2022-10-05_03-03-47.jpg
  (94.3 kB; image/jpeg)
  
  Hi,
  
  I just started using cpseis (looks very promising) and it seems I
  can't modify Length of traces and DT in JOB_DATA.
  
  Right after I change the focus from one of these fields they become
  zeros: 000000000.
  My real dt is 0.004 second and the number of samples is 1500.
  It seems I can set dt to 4 (even though it is displayed as zeros) but
  I'm unable to set it to 0.004.
  I also tried to manually set |DT = "4,E-03"| but this doesn't help.
  
  openjdk 11.0.16
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/cpseis/bugs/141/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  Related
  
  Bugs: #141
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - kerim khemraev - 2022-10-06
    
    I just tried to follow your suggestions but that didnt' help (instead of cd cpsjobs I ran /mnt/HDD_2TB/cpseis_data as I don't have cpsjobs dir).
    
    The output from the suggested commands:
    echo $CPSEISINSTALLDIR: /home/kerim/cpseis
    echo $CPSEISARCH: Linux_x86_64_2.31_gfortran_mpich3
    echo $CPSEIS_COMPILER: gfortran
    
    gfortran --version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    java --version: openjdk 11.0.16 2022-07-19 (I tried to build cpseis both using my preinstalled java and using java that comes with cpseis: nothing helped, I use my preinstalled java)
    Ubuntu 20.04
    
    my .bashrc concerning spseis:
    export THIRDPARTY_DIR="/home/kerim/cpseis/thirdparty"
    export CPSEIS_INSTALL_DIR="/home/kerim/cpseis"
    unset CPSEIS_ENVIRONMENT
    source $CPSEIS_INSTALL_DIR/etc/cpseis_bashrc.sh mpich3 gfortran
    export PATH="${PATH}:${THIRDPARTY_DIR}/mpich-3.2.1/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin"
    export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${THIRDPARTY_DIR}/fftw-2.1.5/platforms/Linux_x86_64_2.31_gfortran/lib"
    export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${THIRDPARTY_DIR}/mpich-3.2.1/platforms/Linux_x86_64_2.31_gfortran_mpich3/lib"
    export CPSEIS_HOME=$CPSEIS_INSTALL_DIR
    export PATH=$PATH:"$CPSEIS_INSTALL_DIR/thirdparty/mpich-3.2.1/platforms/bin"
    export PATH=$PATH:$CPSEIS_INSTALL_DIR
    export PATH=$PATH:"$CPSEIS_INSTALL_DIR/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin"
    export PATH=$PATH:"$CPSEIS_INSTALL_DIR/scripts"
    
    Probably some paths are excessive I didn't check yet
    
    By the way the compilation goes without any errors. Only this one:
    ln: failed to create symbolic link '/home/kerim/cpseis/thirdparty/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/jdk-6u14-linux-x64_x86_64': Permission denied
    
    Last edit: kerim khemraev 2022-10-06
    
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    - Bill Menger - 2022-10-07
      
      I have an ubuntu 20.04 build with your exact kernel and mpich3 and gfortran. My javac is at
      /apps/cpseis/thirdparty/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin/javac where my $CPSEIS_ARCH =
      Linux_x86_64_2.31_gfortran_mpich3. I suggest putting in a link to your jdk something like this:
      
      bmenger@ubuntu:/apps/cpseis/thirdparty/jdk/platforms$ pwd
      
      /apps/cpseis/thirdparty/jdk/platforms
      
      bmenger@ubuntu:/apps/cpseis/thirdparty/jdk/platforms$ ls -ld Linux_x86_64_2.31_gfortran_mpich3
      
      lrwxrwxrwx 1 bmenger bmenger 53 Dec 5 2021 Linux_x86_64_2.31_gfortran_mpich3 ->
      /apps/cpseis/thirdparty/jdk/jdk-6u14-linux-x64_x86_64
      
      bmenger@ubuntu:/apps/cpseis/thirdparty/jdk/platforms$ which javac
      
      /apps/cpseis/thirdparty/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin/javac
      
      bmenger@ubuntu:/apps/cpseis/thirdparty/jdk/platforms$
      
      So. in your $THIRDPARTY_DIR/jdk/platforms you will create a link to your actual java jdk directory and call that link $CPSEIS_ARCH.
      In my case, my jdk is at :
      
      /apps/cpseis/thirdparty/jdk/jdk-6u14-linux-x64_x86_64. My link is called Linux_x86_64_2.31_gfortran_mpich3 and the link is located
      in my $THIRDPARTY_DIR/jdk/platforms directory, which is /apps/cpseis/thirdparty/jdk/platforms.
      
      I'm not sure what else to try unless you want to try using the older version of java that I'm using. There is a bin extract on
      sourceforge on the cpseis project directory.
      
      I tested cfe and it works fine.
      
      Another test for simple functionality is to run the test job file $CPSEIS_INSTALL_DIR/sample_work_files/tiny.wrk by typing:
      
      $ cd $CPSEIS_INSTALL_DIR/sample_work
      
      $ icps tiny.wrk
      
      If it works, then the guts of cpseis are functional. Cfe is the issue.
      
      Bill
      
      From: bugs@cpseis.p.re.sourceforge.net bugs@cpseis.p.re.sourceforge.net On Behalf Of kerim khemraev
      Sent: Thursday, October 6, 2022 4:04 AM
      To: [cpseis:bugs] 141@bugs.cpseis.p.re.sourceforge.net
      Subject: [cpseis:bugs] Re: #141 cfe: unable to set Length of traces and DT in JOB_DATA
      
      I just tried to follow your suggestions but that didnt' help (instead of cd cpsjobs I ran /mnt/HDD_2TB/cpseis_data as I don't have
      cpsjobs dir).
      
      The output from the suggested commands:
      echo $CPSEISINSTALLDIR: /home/kerim/cpseis
      echo $CPSEISARCH: Linux_x86_64_2.31_gfortran_mpich3
      echo $CPSEIS_COMPILER: gfortran
      
      gfortran --version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
      java --version: openjdk 11.0.16 2022-07-19 (I tried to build cpseis both using my preinstalled java and using java that comes with
      cpseis: nothing helped, I use my preinstalled java)
      
      my .bashrc concerning spseis:
      export THIRDPARTY_DIR="/home/kerim/cpseis/thirdparty"
      export CPSEIS_INSTALL_DIR="/home/kerim/cpseis"
      unset CPSEIS_ENVIRONMENT
      source $CPSEIS_INSTALL_DIR/etc/cpseis_bashrc.sh mpich3 gfortran
      export PATH="${PATH}:${THIRDPARTY_DIR}/mpich-3.2.1/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin"
      export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${THIRDPARTY_DIR}/fftw-2.1.5/platforms/Linux_x86_64_2.31_gfortran/lib"
      export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${THIRDPARTY_DIR}/mpich-3.2.1/platforms/Linux_x86_64_2.31_gfortran_mpich3/lib"
      export CPSEIS_HOME=$CPSEIS_INSTALL_DIR
      export PATH=$PATH:"$CPSEIS_INSTALL_DIR/thirdparty/mpich-3.2.1/platforms/bin"
      export PATH=$PATH:$CPSEIS_INSTALL_DIR
      export PATH=$PATH:"$CPSEIS_INSTALL_DIR/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin"
      export PATH=$PATH:"$CPSEIS_INSTALL_DIR/scripts"
      
      Probably some paths are excessive I didn't check yet
      
      By the way the compilation goes without any errors. Only this one:
      ln: failed to create symbolic link
      '/home/kerim/cpseis/thirdparty/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/jdk-6u14-linux-x64_x86_64': Permission denied
      
      [bugs:#141] https://sourceforge.net/p/cpseis/bugs/141/ cfe: unable to set Length of traces and DT in JOB_DATA
      
      Status: open
      Group: v1.0 (example)
      Created: Wed Oct 05, 2022 05:26 PM UTC by kerim khemraev
      Last Updated: Wed Oct 05, 2022 05:27 PM UTC
      Owner: nobody
      Attachments:
      
      2022-10-05_03-03-47.jpg https://sourceforge.net/p/cpseis/bugs/141/attachment/2022-10-05_03-03-47.jpg (94.3 kB;
      image/jpeg)
      
      Hi,
      
      I just started using cpseis (looks very promising) and it seems I can't modify Length of traces and DT in JOB_DATA.
      
      Right after I change the focus from one of these fields they become zeros: 000000000.
      My real dt is 0.004 second and the number of samples is 1500.
      It seems I can set dt to 4 (even though it is displayed as zeros) but I'm unable to set it to 0.004.
      I also tried to manually set DT = "4,E-03" but this doesn't help.
      
      openjdk 11.0.16
      
      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cpseis/bugs/141/
      
      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
      
      Related
      
      Bugs: #141
      
      alternate
      
      If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

kerim khemraev - 2022-10-07

Thank you for the hints, it seems the problem still not solved.

What I tried:

1) I made cpseis to build java that comes with it.
2) Then I added link to it:

cd $THIRDPARTY_DIR/jdk/platforms sudo ln -s $THIRDPARTY_DIR/jdk/jdk-6u14-linux-x64_x86_64 $CPSEIS_ARCH

3) Then I prepended bin dir to the PATH: export PATH="$THIRDPARTY_DIR/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin":$PATH
Now javac -version prints javac 1.6.0_14

4) Then I rebuilt cfe:

cd $CPSEIS_INSTALL_DIR/platforms/$CPSEIS_ARCH make clean;make;make cfe

Still no luck :)

Though one error (highlighted with the red in terminal) during rebuilt I noticed:

------------------------------------------------------- creating makefile.depend in /home/kerim/cpseis/spws_home/programs/isep ------------------------------------------------------- cd /home/kerim/cpseis/spws_home/programs/isep; /home/kerim/cpseis/scripts/make_dependencies "g++ -MM -DLINUX -DLINUXI -D_FILE_OFFSET_BITS=64 -DBETALIB -I/home/kerim/cpseis/spws_home/programs/isep -I/home/kerim/cpseis/include -I/home/kerim/cpseis/spws_home/include -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -I/usr/X11R6/include/X11/SM -I/usr/X11R6/include/X11/ICE -I/usr/X11R6/include/Xm -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -I/usr/include -I/usr/X11R6/include" --> Getting List of fortran90 source files... ls: No match. --> Getting List of c source files... ls: No match. --> Getting List of c++ source files... ls: No match. --> building fortran90 dependencies... --> building XML dependencies... --> assembling compiler command for building c and c++ dependencies... --> building c and c++ dependencies... g++: fatal error: no input files compilation terminated. --> finished --> your dependencies are now in a file called makefile.depend

I tried to run test as you suggested and it worked fine.
Also I could modify my workflow file using text editor and then successfully run it from terminal.

I'm not familiar with fortran but I'm pretty experienced C++ developper and have little knowledge about Java. If you could give me some hints how to inspect Java GUI (how to open it in IDE, in NetBeans for example) probably I could make some efforts a little more.
From fortran I understood that DT and other vars are stored as global. Can't understand how fortran uses Java for GUI. It is very strange for me that in GUI float values are converted to 0000000...

Kerim
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- Bill Menger - 2022-10-07
  
  I don’t know what is going on, but it looks like it may be restricted only to your version of CFE. The output you have listed below does not show any errors of significance. The warnings from the build of isep only affect that program, and it is not very important.
  
  I would concentrate efforts on CFE by going to the build directory for it:
  
  $ cd $CPSEIS_INSTALL_DIR/opencfe/src
  
  (This contains the makefile for your build. )
  
  $ make
  
  (this will rebuild all the java and the fortran-to-java interfaces)
  
  (warnings from Java can be ignored, but any FORTRAN, C, or C++ errors should be examined.)
  
  $ make install
  
  $ cd ../sample_work_files
  
  $ cfe –debug
  
  ==
  
  I’ve added this to the google-group for cpseis to get more feedback and ideas from others.
  
  Bill Menger
  
  To rebuild only CFE and to
  
  From: bugs@cpseis.p.re.sourceforge.net bugs@cpseis.p.re.sourceforge.net On Behalf Of kerim khemraev
  Sent: Friday, October 7, 2022 5:53 AM
  To: [cpseis:bugs] 141@bugs.cpseis.p.re.sourceforge.net
  Subject: [cpseis:bugs] #141 cfe: unable to set Length of traces and DT in JOB_DATA
  
  Thank you for the hints, it seems the problem still not solved.
  
  What I tried:
  
  1) I made cpseis to build java that comes with it.
  2) Then I added link to it:
  
  cd $THIRDPARTY_DIR/jdk/platforms
  sudo ln -s $THIRDPARTY_DIR/jdk/jdk-6u14-linux-x64_x86_64 $CPSEIS_ARCH
  
  3) Then I prepended bin dir to the PATH: export PATH="$THIRDPARTY_DIR/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin":$PATH
  Now javac -version prints javac 1.6.0_14
  
  4) Then I rebuilt cfe:
  
  cd $CPSEIS_INSTALL_DIR/platforms/$CPSEIS_ARCH
  make clean;make;make cfe
  
  Still no luck :)
  
  Though one error (highlighted with the red in terminal) during rebuilt I noticed:
  
  creating makefile.depend in /home/kerim/cpseis/spws_home/programs/isep
  
  cd /home/kerim/cpseis/spws_home/programs/isep; /home/kerim/cpseis/scripts/make_dependencies "g++ -MM -DLINUX -DLINUXI -D_FILE_OFFSET_BITS=64 -DBETALIB -I/home/kerim/cpseis/spws_home/programs/isep -I/home/kerim/cpseis/include -I/home/kerim/cpseis/spws_home/include -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -I/usr/X11R6/include/X11/SM -I/usr/X11R6/include/X11/ICE -I/usr/X11R6/include/Xm -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -I/usr/include -I/usr/X11R6/include"
  --> Getting List of fortran90 source files...
  ls: No match.
  --> Getting List of c source files...
  ls: No match.
  --> Getting List of c++ source files...
  ls: No match.
  --> building fortran90 dependencies...
  --> building XML dependencies...
  --> assembling compiler command for building c and c++ dependencies...
  --> building c and c++ dependencies...
  g++: fatal error: no input files
  compilation terminated.
  --> finished
  --> your dependencies are now in a file called makefile.depend
  
  I tried to run test as you suggested and it worked fine.
  Also I could modify my workflow file using text editor and then successfully run it from terminal.
  
  I'm not familiar with fortran but I'm pretty experienced C++ developper and have little knowledge about Java. If you could give me some hints how to inspect Java GUI (how to open it in IDE, in NetBeans for example) probably I could make some efforts a little more.
  From fortran I understood that DT and other vars are stored as global. Can't understand how fortran uses Java for GUI. It is very strange for me that in GUI float values are converted to 0000000...
  
  Kerim
  
  [bugs:#141] https://sourceforge.net/p/cpseis/bugs/141/ cfe: unable to set Length of traces and DT in JOB_DATA
  
  Status: open
  Group: v1.0 (example)
  Created: Wed Oct 05, 2022 05:26 PM UTC by kerim khemraev
  Last Updated: Thu Oct 06, 2022 09:04 AM UTC
  Owner: nobody
  Attachments:
  
  2022-10-05_03-03-47.jpg https://sourceforge.net/p/cpseis/bugs/141/attachment/2022-10-05_03-03-47.jpg (94.3 kB; image/jpeg)
  
  Hi,
  
  I just started using cpseis (looks very promising) and it seems I can't modify Length of traces and DT in JOB_DATA.
  
  Right after I change the focus from one of these fields they become zeros: 000000000.
  My real dt is 0.004 second and the number of samples is 1500.
  It seems I can set dt to 4 (even though it is displayed as zeros) but I'm unable to set it to 0.004.
  I also tried to manually set DT = "4,E-03" but this doesn't help.
  
  openjdk 11.0.16
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cpseis/bugs/141/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  Related
  
  Bugs: #141
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

kerim khemraev - 2022-10-07

It seems there is no errors during cfe build. And it didn't help.

Launching cfe -debug I noticed that right after I modify the value in DT (sample interval (seconds)) (JOB_DATA) I can see the output in terminal:

int_debugset_value(3, "EnterWindow" , "JOB_DATA" , " "); <EnterWindow keyword="JOB_DATA" windowId="3"/> 10-07 19:31:52 <Message> <Reply/> </Message> int_debugset_value(3, "ModifyField" , "DT" , "0.004"); <ModifyField keyword="DT" windowId="3" value="0.004"/> 10-07 19:31:58 <Message> <Reply> <MODIFYFIELD keyword="DT" windowId="3" value="4,E-03"/> <MODIFYFIELD keyword="NDPT" windowId="3" value="1500"/> </Reply> </Message>

but in GUI the field becomes 000000000 and in textual file .wrk the values are integers: DT = "4,E+00"

By the way it seems this concerns all the GUI input fields accepting float as the similar behaviour in PROJECT_DATA Easting origin, X Grid distance etc.

I just remembered that I also have gcc-11 and gcc-12 compilers in /home/kerim/gcc/11 and /home/kerim/gcc/12 accordingly.
And in .bashrc I also have:

export CC=/home/kerim/gcc/11/bin/gcc export CXX=/home/kerim/gcc/11/bin/g++ export LD_LIBRARY_PATH=/home/kerim/gcc/11/lib64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/home/kerim/gcc/12/lib64:$LD_LIBRARY_PATH

I will try to rebuild cpseis with these four lines commented.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Bill Menger - 2022-10-08
  
  I rebuilt cfe on Ubuntu 20.04 but am using gcc and g++ version 9.04. When run in debug mode, I see the same messages you do (below
  in your snippet of a log file), but my display works fine. Something is not correct in how the values from <modifyfield.> are being
  stored and retransmitted back to the GUI. The way the GUI communicates with the cpseis engine is via messaging. This was written
  ~1999 when the SOAP protocols were being discussed. We initially built the model to run across slow modems so the GUI would live in
  the user's home terminal and the engine would live on the linux cluster/workstation back at the office. So, messaging was the easy
  way to make this work. The fact that you are getting the message sent from the GUI to the engine</modifyfield.>
  
  int_debugset_value(3, "ModifyField" , "DT" , "0.004");
  and received back from the engine to the GUI
  <modifyfield keyword="DT" windowid="3" value="0.004">
  Indicates that the code is running correctly, but somehow the floats are being mangled before displaying back to the GUI.</modifyfield>
  
  My only suggestion at this point is to attempt to downgrade gcc/g++ to 9.04 and try rebuilding from the opencfe/src directory again,
  with a "make; make install".
  Bill
  
  From: bugs@cpseis.p.re.sourceforge.net bugs@cpseis.p.re.sourceforge.net On Behalf Of kerim khemraev
  Sent: Friday, October 7, 2022 12:11 PM
  To: [cpseis:bugs] 141@bugs.cpseis.p.re.sourceforge.net
  Subject: [cpseis:bugs] #141 cfe: unable to set Length of traces and DT in JOB_DATA
  
  It seems there is no errors during cfe build. And it didn't help.
  
  Launching cfe -debug I noticed that right after I modify the value in DT (sample interval (seconds)) (JOB_DATA) I can see the output
  in terminal:
  
  int_debugset_value(3, "EnterWindow" , "JOB_DATA" , " ");
  <enterwindow keyword="JOB_DATA" windowid="3"></enterwindow>
  
  10-07 19:31:52
  
  <message>
  <reply>
  </reply></message>
  
  int_debugset_value(3, "ModifyField" , "DT" , "0.004");
  <modifyfield keyword="DT" windowid="3" value="0.004"></modifyfield>
  
  10-07 19:31:58
  
  <message>
  <reply>
  <modifyfield keyword="DT" windowid="3" value="4,E-03">
  <modifyfield keyword="NDPT" windowid="3" value="1500">
  </modifyfield></modifyfield></reply>
  </message>
  
  but in GUI the field becomes 000000000 and in textual file .wrk the values are integers: DT = "4,E+00"
  
  By the way it seems this concerns all the GUI input fields accepting float as the similar behaviour in PROJECT_DATA Easting origin,
  X Grid distance etc.
  
  I just remembered that I also have gcc-11 and gcc-12 compilers in /home/kerim/gcc/11 and /home/kerim/gcc/12 accordingly.
  And in .bashrc I also have:
  
  export CC=/home/kerim/gcc/11/bin/gcc
  export CXX=/home/kerim/gcc/11/bin/g++
  export LD_LIBRARY_PATH=/home/kerim/gcc/11/lib64:$LD_LIBRARY_PATH
  export LD_LIBRARY_PATH=/home/kerim/gcc/12/lib64:$LD_LIBRARY_PATH
  
  I will try to rebuild cpseis with these four lines commented.
  
  [bugs:#141] https://sourceforge.net/p/cpseis/bugs/141/ cfe: unable to set Length of traces and DT in JOB_DATA
  
  Status: open
  Group: v1.0 (example)
  Created: Wed Oct 05, 2022 05:26 PM UTC by kerim khemraev
  Last Updated: Fri Oct 07, 2022 10:53 AM UTC
  Owner: nobody
  Attachments:
  
  2022-10-05_03-03-47.jpg https://sourceforge.net/p/cpseis/bugs/141/attachment/2022-10-05_03-03-47.jpg (94.3 kB;
  image/jpeg)
  
  Hi,
  
  I just started using cpseis (looks very promising) and it seems I can't modify Length of traces and DT in JOB_DATA.
  
  Right after I change the focus from one of these fields they become zeros: 000000000.
  My real dt is 0.004 second and the number of samples is 1500.
  It seems I can set dt to 4 (even though it is displayed as zeros) but I'm unable to set it to 0.004.
  I also tried to manually set DT = "4,E-03" but this doesn't help.
  
  openjdk 11.0.16
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/cpseis/bugs/141/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  Related
  
  Bugs: #141
  
  alternate
  
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kerim khemraev - 2022-10-07

No, rebuilding with commented earlier mentioned gcc-11/12 CC/CXX and LD_LIBRARY_PATH vars didn't help.

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seismick - 2022-10-08

Sorry I only just saw this bug report. I have built cfe with Oracle java 6-18 and openjdk 8,11,17 and didn't get this issue. I have encountered a problem with cfe parameter entry with gfortran version 9 or later with optimisation. The parameters pass through a chain of Fortran subroutines and something is corrupted with newer gfortran. I have not been able to figure out the cause. So the installation script will unfortunately set -O0 if gcc version is greater than 8. So I have been using Centos 8, Debian 10, and other old distros. I will try an installation with gcc 9+ to see if I can reproduce this.

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seismick - 2022-10-08

I tried two builds: Alma linux 9 with gcc 11.2 and openjdk 11.0.16 and Mint linux 20.3 with gcc 9.4 and openjdk 11.0.16. I found no problem with cfe. Both had CPSeis revision 261. Then I rebuilt in Mint with revision 268 and cfe still works.
I checked the make depend log and the message
g++: fatal error: no input files
comes up for isep and a few other programs. So that is a red herring.

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kerim khemraev - 2022-10-09

That is very strange.

I just compiled gcc with gfortran 8.5, removed mpich with sudo apt-get purge --auto-remove mpich and the problem wasn't solved.

I will try to build cpseis on virtual machine.

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kerim khemraev - 2022-10-09

I just tested on RedOS 7.3 (based on Centos 7 as far as I know) using VirtualBox and it works fine!

Thus it must be something with Ubuntu 20.04 setup.
I will try to get known with cpseis on RedOS and probably later will come back to the problem.

Thank you for your efforts!

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seismick - 2022-10-09

This is turning into a real mystery. One possibility is different versions of java for compile and runtime. If you do these commands, what do you see?
which java
which javac
java -version
javac -version

And what desktop are you using in Ubuntu (and X11 or Wayland)?

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kerim khemraev - 2022-10-09

Here are otputs from the commads with resolved links:
which java: /usr/lib/jvm/java-11-openjdk-amd64/bin/java
which javac: /usr/lib/jvm/java-11-openjdk-amd64/bin/javac
**java -version: **

openjdk version "11.0.16" 2022-07-19 OpenJDK Runtime Environment (build 11.0.16+8-post-Ubuntu-0ubuntu120.04) OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)

javac -version: javac 11.0.16

I use x11 Ubuntu. To check that I've used the commad loginctl show-session c1 -p Typewhere c1 is my session ID
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seismick - 2022-10-10

I tried to recreate your situation as closely as possible. Ubuntu 20.04, mpich3 and Sun JDK6.14 and used your .bashrc, but cfe still works for me. Just curious about one error message you got;
/home/kerim/cpseis/thirdparty/jdk/platforms/Linux_x86_64_2.31_gfortran_mpich3/jdk-6u14-linux-x64_x86_64': Permission denied
Whenever I rebuild CPSeis it just says the java link already exists rather than permission denied.
Also noticed you have some duplicates in your PATH. If you run the attached script, you can see if you wish to trim some of them.

paths.sh

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@seismick I cleaned a little bit the env vars.

I just deleted and cloned cpseis dir once again.
I still see the mentionned error " unable to create link...

I digged to the install_cpseis script and at line 167 we have ln -s -f \$UJL \$CPSEIS_ARCH.
I slighty modified this snippet:

ERROR=0
# links thirdparty to existing JDK 
if ! [ -x "$(command -v javac)" ]; then
 echo >&2 "*** javac not installed ***"
else
 varwj=\$(realpath $(which javac))
 export UJL=\${varwj%/bin/javac}
 echo "I have preinstalled javac"
 echo "varwj:" $varwj
 echo "UJL (within if/else statement):" $UJL
fi
# java home maybe "/usr/java/latest" or "/usr/lib/jvm/default"
cd  \$THIRDPARTY_DIR
mkdir -p jdk/platforms
#
cd jdk/platforms
echo "UJL:" $UJL
echo "CPSEIS_ARCH:" $CPSEIS_ARCH
pwd
ln -s -f \$UJL \$CPSEIS_ARCH

and the output is:

I have preinstalled javac
varwj:
UJL (within if/else statement):
UJL:
CPSEIS_ARCH: Linux_x86_64_2.31_gfortran_mpich3
/home/kerim/cpseis/thirdparty/jdk/platforms
ln: failed to create symbolic link 'Linux_x86_64_2.31_gfortran_mpich3/java-11-openjdk-amd64': Permission denied
Hit return to continue

as you can see UJL and varwj are empty.

If I type those commands in terminal manually then I get:

varwj: /usr/lib/jvm/java-11-openjdk-amd64/bin/javac
UJL: /usr/lib/jvm/java-11-openjdk-amd64

Is there any reason why those vars are not exported?
I just created those links manually and continued the building prrocess.

Now I got other errors:

gfortran installed at: /usr/bin
mpich3 not set up and in your path
URL transformed to HTTPS due to an HSTS policy
--2022-10-10 18:46:45--  https://www.mpich.org/static/downloads/3.2.1/mpich-3.2.1.tar.gz
Resolving www.mpich.org (www.mpich.org)... 140.221.25.3
Connecting to www.mpich.org (www.mpich.org)|140.221.25.3|:443... connected.
WARNING: no certificate subject alternative name matches
    requested host name ‘www.mpich.org’.
HTTP request sent, awaiting response... 404 Not Found
2022-10-10 18:46:46 ERROR 404: Not Found.

tar (child): mpich-3.2.1.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
tar (child): mpich-3.2.1.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
/home/kerim/cpseis/scripts/build_mpich3.sh: line 64: cd: /home/kerim/cpseis/thirdparty/mpich-3.2.1: No such file or directory
/home/kerim/cpseis/scripts/build_mpich3.sh: line 69: cd: /home/kerim/cpseis/thirdparty/mpich-3.2.1: No such file or directory
/home/kerim/cpseis/scripts/build_mpich3.sh: line 83: ./configure: No such file or directory
Build mpich3 complete. Add /home/kerim/cpseis/thirdparty/mpich-3.2.1/platforms/Linux_x86_64_2.31_gfortran_mpich3/bin to your path.
basename: missing operand
Try 'basename --help' for more information.
basename: missing operand
Try 'basename --help' for more information.
Error detected.  Hit return to exit

It is first time I get these errors. I'm googling them now.

kerim khemraev - 2022-10-10

After I recompiled with manula adding link as I mentioned in previous post the problem still exists.

Now I use gcc-9.4, gfortran-9.4, preinstalled java 11.0.16

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cfe: unable to set Length of traces and DT in JOB_DATA

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