Linux installation error [solved]

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manosmat
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Joined: Thu Sep 08, 2022 1:05 pm

Linux installation error [solved]

Post by manosmat »

Hello everyone,

I'm using Linux Mint 20.2 and try to install geopsy. After successful troubleshooting Qt libraries and geopsy version conflict (warning about older Qt version), I'm trying to install geopsy v3.4.2, but I receive the following errors, as depicted bellow in the attached image.

Any ideas how to solve it? Should I check and re-install the prerequisites ?

Regards,


Manos
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admin
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Re: Linux installation error

Post by admin »

Hi Manos,

You can add "-skip-openblas" in the configure command line.
Some processes might be sub-optimal with this option but you will solve your compilation error.

Best regards,

Marc
manosmat
Posts: 4
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Re: Linux installation error

Post by manosmat »

Hello, thanks for your reply!

When I add the "-skip-openblas" command you mentioned, the following message appears.

The "-skip" command is not recognized, and as far as I can tell, I should add something like "--ignore-errors" and/or "--keep-going". Any thoughts on how to proceed?

Sorry for asking something that might be obvious and trivial, but while trying to configure Qt libraries, I ended up installing Linux again. Twice. :)

Regards,


Manos
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admin
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Re: Linux installation error

Post by admin »

Hi Manos,

You have to add the option "-skip-openblas" to the configure step. In your snapshot, you added it the make step. A single "-" not a double is required.

Best regards,

Marc
manosmat
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Re: Linux installation error

Post by manosmat »

Well, I tried both, single "-" and double "--", I just put the screenshot from the latter.

When adding "-skip-openblas" option to make command, then after the options list shown above, I got all these extra #environment information, and also some more.

Does this means I'm OK with installation?

Greetings,


Manos
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admin
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Re: Linux installation error

Post by admin »

No, you are not done.
You cannot add this option to the make command. It is not recognized as a make option. You have to add it to the configure command one step before the make command.

Best regards,

Marc
manosmat
Posts: 4
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Re: Linux installation error

Post by manosmat »

Hi Marc, and thank you for answering immediately. I appreciate that.

Yes, my mistake: I should have add "-skip-openblas" to configure command and not at make.

But is not recognized as an option for configure as well. Attached you may see the "Bad option.." message I get.

Nevertheless, I also apt install "libopenblas-dev" package again, so now I'm trying commands configure (without adding "-skip-openblas"), make and make install. Then I receive more error and fatal error messages, as seen in attached figure.

Following the troubleshooting of that post, I also tried make -i in order to ignore the errors. Then the installation process takes a bit longer, with many more errors and fatal errors coming out. I can tell that there is no space left on the partition.

How much space is needed for the installation of geopsy?

Thanks in advance. I'm really trying to make things work for my thesis, so I appreciate your help.
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Last edited by manosmat on Sat Oct 01, 2022 6:24 pm, edited 2 times in total.
admin
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Re: Linux installation error

Post by admin »

Hi Manos,

Try to run

Code: Select all

make clean
before running the usual

Code: Select all

make
The change you made to OpenBlas library requires the update of pre-compiled headers.
When you send terminal errors, copy and submit the text (e.g. inside <code> </code> tags) rather than a snapshot.

Best regards,

Marc
manosmat
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Re: Linux installation error

Post by manosmat »

Hello Marc,

Thank you once again for your answer. By first typing:

Code: Select all

make clean
things seemed to go better, but after a time and before installing finishes, it seems that I'm actually running out of space. :)

Therefore, I actually format everything and now I'm running under Ubuntu 22.04.1 LTS, with a little more space.

I'm installing prerequisites but 'qt5-base-dev' package returns:

Code: Select all

Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
E: Unable to locate package qt5-base-dev
Anyway, my Qt versions seems to be:
qmake -v
QMake version 3.1
Using Qt version 5.15.3 in /usr/lib/x86_64-linux-gnu
But when I'm trying to ./configure geopsy, I get several times the following message:

Code: Select all

Configure gpreplace
Configure gpsh
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
Configure gpmt
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
lrelease: could not exec '/usr/lib/qt5/bin/lrelease': No such file or directory
It seems Qt libraries are stored somewhere else. Should I change something, or is it OK to continue with 'make' command? Should I update PATH in .profile for Qt libraries? Any ideas how to continue?
Last edited by manosmat on Fri Oct 07, 2022 4:11 am, edited 1 time in total.
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Re: Linux installation error

Post by admin »

With new Linux distribution releases packaging is sometimes changing. qt5-base-dev probably disappeared. I have to update the documentation. Apparently Qt is installed which is the most important point.

The error message you get is related to lrelease. From the information I could get from Ubuntu man pages, it is shipped with package qttools5-dev-tools. Can you check if it is installed? Then, restart configure.

Best regards,

Marc
manosmat
Posts: 4
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Re: Linux installation error

Post by manosmat »

Hi again,
Apparently Qt is installed which is the most important point.
Yes, but is was only after installing package qttools5-dev-tools when qmake -version command returned:
QMake version 3.1
Using Qt version 5.15.3 in /usr/lib/x86_64-linux-gnu
Anyway, commands:

Code: Select all

make -j 8
and

Code: Select all

make install -C /path/where/i/wanted/to/build
both finished without error message this time :-)

I have two more questions:

1. Under Variable environment is mentioned to add
export PATH=/usr/local/Geopsy.org/bin:$PATH
to .profile

Should I add bin path of
/home/manosmat/Geopsy/build/bin/
or
/home/manosmat/Geopsy/install/bin/
2. After completing installation, how do I start using geopsy? I cannot see any application icon or shortcut added anywhere. Is it something else to be done, apart from PATH configuration?
Last edited by manosmat on Fri Oct 07, 2022 4:27 pm, edited 2 times in total.
admin
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Re: Linux installation error

Post by admin »

Hi Manos,

Good to read that you got to the end.
You have to add

Code: Select all

export PATH=/home/manosmat/Geopsy/install/bin:$PATH
Binaries in their build location are not usable. Paths for searching libraries are correct only in the "install" directory.

Once you source your .profile or if you restart a new terminal, you can simply type

Code: Select all

$ geopsy 
If you want to know which binary file is executed, run

Code: Select all

$ which geopsy
/usr/local/Geopsy.org/3.5/Debug/bin/geopsy # in my local case
To get the list of all applications provided by the package:

Code: Select all

ls /usr/local/Geopsy.org/3.5/Debug/bin
manosmat
Posts: 4
Joined: Thu Sep 08, 2022 1:05 pm

Re: Linux installation error

Post by manosmat »

Only if I first source .profile, it was possible to start geopsy. But after restarting, by simply typing geopsy to the terminal, application ~finally~ starts! :D

I get the following warning though, I'm not sure if it's fine.

Code: Select all

manosmat@manosmat-Inspiron-3583:~$ geopsy
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
And for the record, I receive the following, when typing what you suggested.

Code: Select all

manosmat@manosmat-Inspiron-3583:~$ which geopsy
/home/manosmat/Geopsy/install/bin//geopsy

Code: Select all

manosmat@manosmat-Inspiron-3583:~$ ls /home/manosmat/Geopsy/install/bin/
dinver       gpdc           gpgroup2phase  gprandom   gpviewdcreport
figue        gpdcmisfit     gphistogram    gprefra    gpviewmax
geopsy       gpdcreport     gplivemodel    gpreplace  gpvoronoi
geopsy-fk    gpdepths       gpmaplayer     gpsh       max2curve
geopsy-hv    gpdistance     gpmodel2param  gpsignal   screenpicker
GeopsyLand   gpec8          gpmt           gpsort     spac2disp
geopsy-spac  gpell          gpparam2model  gpspac     vslarray
gpcoord      gpfksimulator  gppoisson      gptarget   waran
gpcurve      gpgridsearch   gpprofile      gptime     warangps
What I also did differently this time, was to firstly install Qt libraries as referred in documentation , and then installing MATLAB(2014b), which comes with its own Qt packages and they seem to interfere with newer versions of Qt.

My main concern was to have dinver installed and working, in order to run SWIP, but I still have things to troubleshoot.

Thanks for the support!
manosmat
Posts: 4
Joined: Thu Sep 08, 2022 1:05 pm

Re: Linux installation error [solved]

Post by manosmat »

Hello again,

When starting geopsy, I get the following warning:
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Although the program starts and I have made it to use active fk method up to dinver results, when trying to process something bigger, i.e multiple .dat recordings to convert signals, then the following fatal error appears:

Code: Select all

<CrashReport>
<Error>
<severity>--FATAL ERROR- </severity>
<message>Segmentation fault Signal</message>
<time>2022-11-22 19:47:42.153</time>
<threads>main,layerPainter1,layerPainter2,layerPainter3,layerPainter4,layerPainter5,layerPainter6,layerPainter7,layerPainter8</threads>
<currentThread>main thread</currentThread>
<stack>QGpCoreTools::CoreApplicationPrivate::backTrace()
QGpCoreTools::CoreApplicationPrivate::bugInfo(QGpCoreTools::Message::Severity, QString const&amp;)
QGpCoreTools::CoreApplicationPrivate::reportBugNow(QGpCoreTools::Message::Severity, QString const&amp;)
QGpCoreTools::CoreApplicationPrivate::osSignal(int)

GeopsyCore::SubSignalPool::writeSeg2TextHeader(QFile&amp;, double&amp;) const
GeopsyCore::SubSignalPool::saveSeg2(QString) const
GeopsyCore::SubSignalPool::save(QString, bool, GeopsyCore::SignalFileFormat, int, QString const&amp;) const
MainWindow::exportSignal()

QAction::triggered(bool)
QAction::activate(QAction::ActionEvent)


QWidget::event(QEvent*)
QApplicationPrivate::notify_helper(QObject*, QEvent*)
QApplication::notify(QObject*, QEvent*)
QCoreApplication::notifyInternal2(QObject*, QEvent*)
QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&lt;QWidget&gt;&amp;, bool, bool)


QApplicationPrivate::notify_helper(QObject*, QEvent*)
QCoreApplication::notifyInternal2(QObject*, QEvent*)
QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*)
QWindowSystemInterface::sendWindowSystemEvents(QFlags&lt;QEventLoop::ProcessEventsFlag&gt;)




QEventDispatcherGlib::processEvents(QFlags&lt;QEventLoop::ProcessEventsFlag&gt;)
QEventLoop::exec(QFlags&lt;QEventLoop::ProcessEventsFlag&gt;)
QCoreApplication::exec()
modeGui(int, char**, bool)




</stack>
<bugStack>---- thread main
---- thread layerPainter1
---- thread layerPainter2
---- thread layerPainter3
---- thread layerPainter4
---- thread layerPainter5
---- thread layerPainter6
---- thread layerPainter7
---- thread layerPainter8
---- thread main
---- thread layerPainter1
---- thread layerPainter2
---- thread layerPainter3
---- thread layerPainter4
---- thread layerPainter5
---- thread layerPainter6
---- thread layerPainter7
---- thread layerPainter8
</bugStack>
</Error>
<application>geopsy</application>
<version>  Qt                  5.15.3
  QGpCoreTools        2.4.1 from 3.4.2-preview
      (commit dfac7b4dc2205e501fd42412c5281d2038666b30)
  QGpCoreMath         1.4.1 from 3.4.2-preview
      (commit 85b36aae01500a9f560e99838a51570cca13326f)
  GeopsyCore          4.4.1 from 3.4.2-preview
      (commit 6991560c3cf82dfd60b7b38a8a23259d1f2c6218)
  GeopsySLink         2.0.3 from 3.4.2-preview
      (commit 2f01f562d775a4ddcdfc6a3b388c2ecb0cbb3a9a)
  QGpGuiTools         2.4.1 from 3.4.2-preview
      (commit 59782a4c579e510600bf90f355d368b0a70c9b80)
  SciFigs             3.3.1 from 3.4.2-preview
      (commit e8084e18ad59a0802cf80ba7e5f99fa2dcf656d9)
  GeopsySLinkGui      2.0.2 from 3.4.2-preview
      (commit f6e61f2761b9ab1fa13c821e2a94732db60abf4f)
  QGpGuiMath          1.3.1 from 3.4.2-preview
      (commit 8e80e068f4f3b16a30e8fb8dff21177f25a58da6)
  GeopsyGui           3.4.0 from 3.4.2-preview
      (commit d6c09f3739dd7578f652f0cf0ab2a0261abfa9bb)
  geopsy              3.3.3 from 3.4.2-preview
      (commit fb3d54b85a28e6ba741794e0cb6666d0b25c0167)
  geopsyfigs          1.0.2 from 3.4.2-preview
      (commit 33697385e465d0d0ec4344aba55058811e934918)
  campbelltob3        1.0.1 from 3.4.2-preview
      (commit 6e12f8024f0a052e430878492367702311588147)
  DinverCore          1.3.0 from 3.4.2-preview
      (commit 9ec8f3f7c81a7677f85b24cd0fd270add0d70b7d)
  QGpCoreStat         1.2.1 from 3.4.2-preview
      (commit c1b755f5085e2eb75d080f579f308f853ed04997)
  QGpCoreWave         2.2.0 from 3.4.2-preview
      (commit 18e08f9fd358a9e504047ec288ca4ab71a7c9851)
  QGpCompatibility    1.1.1 from 3.4.2-preview
      (commit 790b5d534791ec172ac8ae79e014c9f21638f03f)
  DinverDCCore        2.2.0 from 3.4.2-preview
      (commit 654cab13b392853128bb5fa90891ecf10b5c3f0c)
  QGpGuiWave          1.2.1 from 3.4.2-preview
      (commit 2889d6a23de9671c33c0ae088b33e537035df26f)
  ArrayCore           4.1.1 from 3.4.2-preview
      (commit da5964dea91a019ce673ac10d5454dd791c7b479)
  ArrayGui            1.3.0 from 3.4.2-preview
      (commit bb09428d0df9ad7ab7996d50f8ac067b450a9bec)
  geopsyarray         3.2.3 from 3.4.2-preview
      (commit 232748e77e65b8ac3900e9dd365559ba07e1a182)
  geopsydamping       2.1.2 from 3.4.2-preview
      (commit 42138a483fb28eb47b24cf53b4c1822c5d2f7c8b)
  HVCore              1.1.1 from 3.4.2-preview
      (commit 74d0c5c0fb0ae5e8fb195f7b31ac0202c1642057)
  HVGui               1.1.0 from 3.4.2-preview
      (commit a66df7fe63f6c9107cfffcd4fa86d4f9893fec16)
  geopsyhv            4.0.2 from 3.4.2-preview
      (commit ecd96a31c8abadf86bcbae0dd02bb37935b26dc7)
  geopsynr            1.1.1 from 3.4.2-preview
      (commit f149a70197f8622e594ecec09f55068ecabcfc33)
  geopsyptmotion      2.0.3 from 3.4.2-preview
      (commit c82034566f860b11afdc973ca84ef0027af6cf95)
  geopsyrefra         2.0.2 from 3.4.2-preview
      (commit 807393bf66c9762a914de2cbc8c43813d8ae4227)
  geopsytfa           2.1.1 from 3.4.2-preview
      (commit b87f1cb860bedfd6fb8d0439e749dd7464b26a24)
  hvtfa               2.1.2 from 3.4.2-preview
      (commit 02bfceef408e95d27320ad7d3b857f737363640d)
  matfiles            1.0.3 from 3.4.2-preview
      (commit aa4bbdecc6f645ece0598270993e17766e4c7b32)
  phaseit             1.0.1 from 3.4.2-preview
      (commit 6f91cccebacc25109780c4389f47dd5b6766dd30)
</version>
<system>ubuntu 22.04</system>
</CrashReport>
And geopsy terminates. Are the warning in the terminal and the above fatal error anyhow related? Any thoughts?

Kind regards!
Last edited by manosmat on Tue Nov 22, 2022 8:16 pm, edited 2 times in total.
admin
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Re: Linux installation error [solved]

Post by admin »

Hi,

Thanks for your bug report. There is no link between the warning and the crash you experienced.
You can safely ignore it.
For the crash, I'm curious about the details. I tried to reproduce it but without success. Can you reproduce it? Show a table and a graphic of the signals you want to export in snapshots.

Best regards,
Marc
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