Virtual machines

Hello to everyone and the Terrascope team,

I've just receive the answer that I was allocated a VM, but I can't connect to it with the port number and the server address gave in the e-mail. I tried with my account login and and without login, just with the server address, but nothing works. I use the ubuntu command line as i don't really need the graphic interface. And the status of my VM in my account is indicated "Active", so I don't really know whether it's coming from my end or the VM end... :)

Thank you very much for your help.

Daria

Please keep the Terrascope Platform safe. Please spread this message to the Terrascope Team of VITO (Please let every member of Terrascope Platform be aware of this situation). There're some information I think I may need to share with you VITO guys.  (You can check my detailed post here: https://snowice.yourenvybook.ml/please-keep-terrascope-safe.html)

Hi, there !

My name's Ian and I couldn't access my VM through SSH (Or X2GO), it has been 2 weeks since 2nd, Feb. I do need some help.  

First I thought it's a network issue, but I tried with the WIFI of my home and even with the network of my friends in the past two weeks.

I've already checked my SSH keys and rebooted the VM (By the VM Dashboard) for several times, it still did not work. 

I've already backed up import datasets and wish you guys could reset the VM or rebuild the VM.

Please help !

My account name: lmodukrua@uservm.terrascope.be

When I started my VM I get this message

disks on harjit9090 is UNKNOWN! Info:    Remote Icinga instance 'harjit9090.uservm.rscloud.vito.be' is not connected to 'icinga.intern.vgt.vito.be' When:    2022-05-13 15:25:36 +0200 Service: disks Host:    harjit9090.uservm.rscloud.vito.be Groups:   uservms, uservm_prd IPv4:    192.168.116.80 Comment by icinga-admin:   The root disk on your PROBA-V MEP/Terrascope is almost full. Please use the $HOME/Private and $HOME/Public folders to store your data. If the root disk is full, you won't be able to login anymore.

Hi there, 

I am tyring to use gfortran to compile my FORTRAN code with the options like

gfortran test.f90 -o test_nc.exe -I/usr/include -lnetcdff

I got error of 

Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No such file or directory

I think this relates to the installed version, So I checked it with the command

nc-config --all

And I got the following, Is it possible to have a netCDF version that also supports gFortran? 

Thx!

This netCDF 4.3.3.1 has been built with the following features:

  --cc        -> gcc   --cflags    ->  -I/usr/include -I/usr/include/hdf   --libs      ->

  --has-c++   -> no   --cxx       ->   --has-c++4  -> no   --cxx4      ->

  --fc        ->   --fflags    ->   --flibs     ->   --has-f90   -> no

  --has-dap   -> yes   --has-nc2   -> yes   --has-nc4   -> yes   --has-hdf5  -> yes   --has-hdf4  -> yes   --has-pnetcdf-> no

  --prefix    -> /usr   --includedir-> /usr/include   --version   -> netCDF 4.3.3.1

Hello,

I created a Docker image following the guide, and uploaded it to a private Docker Hub registry account. When I try to send a script via spark-submit, I get an error with the following message. If I try a public image I don't get this problem, so I guess I need to enter my login information somewhere. Is it possible to do this? Or do I need to upload my images somewhere else?

Application report for application_1640081147608_3034 (state: FAILED)

21/12/22 14:22:32 INFO Client:          client token: N/A          diagnostics: Application application_1640081147608_3034 failed 1 times (global limit =2; local limit is =1) due to AM Container for appattempt_1640081147608_3034_000001 exited

with  exitCode: 7

Failing this attempt.Diagnostics: [2021-12-22 14:22:26.758]Exception from container-launch.

Container id: container_e5006_1640081147608_3034_01_000001

Exit code: 7

Exception message: Launch container failed

Shell error output: image: registry.hub.docker.com/flucio/gedap is not trusted.

Disable mount volume for untrusted image

image: registry.hub.docker.com/flucio/gedap is not trusted.

Disable mount volume for untrusted image

image: registry.hub.docker.com/flucio/gedap is not trusted.

Disable cap-add for untrusted image

Docker capability disabled for untrusted image

Unable to find image 'registry.hub.docker.com/flucio/gedap:latest' locally

/usr/bin/docker: Error response from daemon: pull access denied for registry.hub.docker.com/flucio/gedap, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.

See '/usr/bin/docker run --help'.

Shell output: main : command provided 4

main : run as user is luciof

main : requested yarn user is luciof

Creating script paths...

Creating local dirs...

Getting exit code file...

Changing effective user to root...

Wrote the exit code 7 to /data3/hadoop/yarn/local/nmPrivate/application_1640081147608_3034/container_e5006_1640081147608_3034_01_000001

/container_e5006_1640081147608_3034_01_000001.pid.exitcode

[2021-12-22 14:22:26.780]Container exited with a non-zero exit code 7.

[2021-12-22 14:22:26.782]Container exited with a non-zero exit code 7.

For more detailed output, check the application tracking page: https://epod-master2.vgt.vito.be:8090/cluster/app/application_1640081147608_3034 Then click on links to logs of each attempt.. Failing the application.

         ApplicationMaster host: N/A

         ApplicationMaster RPC port: -1

         queue: default

         start time: 1640179342928

         final status: FAILED

         tracking URL: https://epod-master2.vgt.vito.be:8090/cluster/app/application_1640081147608_3034

         user: luciof

21/12/22 14:22:32 INFO Client: Deleted staging directory hdfs://hacluster/user/luciof/.sparkStaging/application_1640081147608_3034

Exception in thread "main" org.apache.spark.SparkException: Application application_1640081147608_3034 finished with failed status

        at org.apache.spark.deploy.yarn.Client.run(Client.scala:1269)

        at org.apache.spark.deploy.yarn.YarnClusterApplication.start(Client.scala:1627)

        at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:904)

        at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:198)

        at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:228)

        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:137)

        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)

Hello everybody, I am experiencing some issues with getting access to my VM through X2Go. I have followed the steps on https://docs.terrascope.be/#/Developers/VirtualEnvironments/VirtualMachines?id=setting-up-x2go-to-use-the-key-pair but when I am logging in to start a session, I receive the error "The remote proxy closed the connection while negotiating the session. This may be due to the wrong authentication credentials passed to the server." I am however sure that I am using the right username and password because I have no issue getting access through putty. I also tried to manually delete my X2Go session through putty with x2goterminate-session, but I still receive the error.

Hello,

Is it possible to  install any other software if required?

Thanks!

Hello everyone,

<br><br>

I'm trying to run processes from the Sentinel 1 toolbox of SNAP in the Terrascope VM, but I keep getting this or similar errors: `RuntimeError: Executing processing graph org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V`. A corresponding forum thread [1] suggests there is a problem with the SNAP version or the package libgfortran3, so I updated SNAP to 8.0.5 and tried installing available libgfortran packages (`sudo yum install -y libgfortran.x86_64 libgfortran-static.x86_64 libgfortran4.x86_64 libgfortran5.x86_64`), but it didn't help.

<br><br>

This is the case for trying to run a coherence process via the SNAP GUI, and also for running SNAP via the gpt tool of the Python pyroSAR package.

<br><br>

I'm wondering if anyone has experience with the S1tbx on the VM, or if this error ever occurred before? If not, it would be greatly appreciated if someone would take the time to try and reproduce my error. I put my workflow here [2]. When I load this graph into the graph tool of SNAP, it doesn't run and throws an error for the coherence process (see error message above). Does it do that on other machines as well?

<br><br>

Thank you in advance and best regards,

<br><br>

Jonathan

<br><br>

[1] https://forum.step.esa.int/t/error-in-sar-image-corregistration-error-nodeld-createstack-org-jblas-nativeblas-dgemm-cciiid-dii-diid-dii-v/12023

<br><br>

[2] https://github.com/jonathom/coherence-docs/blob/master/SNAP_workflow.xml

<br><br>

P.S.: I tried to structure this via html tags, ignore if it didn't work..

Hello all,

I am trying to install the pyroSAR package via `pip install --user pyroSAR` to quickly process Sentinel 1 SLC data via SNAP in a Terrascope VM. The installation produces the following error:

```

    Error: pg_config executable not found.          pg_config is required to build psycopg2 from source.  Please add the directory     containing pg_config to the $PATH or specify the full executable path with the     option:              python setup.py build_ext --pg-config /path/to/pg_config build ...          or with the pg_config option in 'setup.cfg'.          If you prefer to avoid building psycopg2 from source, please install the PyPI     'psycopg2-binary' package instead.

```

Installing psycopg2-binary didn't lead anywhere so I'll have to add the path to `pg_config`. Except I can't find it anywhere (also due to permission restrictions) / am not even sure it is installed. Could you help me identify the file?

If the file isn't there, forum people [1] suggested to install libpq-dev, but I don't have the rights to install packages, do I?

Hope you can help me with this,

Jonathan

[1] https://stackoverflow.com/questions/11618898/pg-config-executable-not-found