Linux install?? #111
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mmcintosh
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Certainly! Just follow the installation instructions. If your Ubuntu version already includes Anaconda, you can proceed from step 2. |
CameronBodine
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I do have anaconda installed version conda 4.12.0 and I have attempted to install and get a few errors that I think are environmental issues one was an upgrade to conda and pip so I back tracked and looked in the ubuntu directory adn tried to follow the directions there: This produced and error as well so I tried upgrading pip as expressed at the bottom of the code listed below. I then tried running the first test again. python test_PINGMapper.py 1 getting this response Attempts to install the missing module request failed as well I assume I have the module name wrong |
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Thanks for the report and sorry that you are having issues. Note that I do most of the development and testing of PING-Mapper on Ubuntu, so I can confirm that it does work. I confess I am a bit confused about your troubleshooting steps. It seems you had to bounce around and tried a few things and it is not clear what caused an error and what the error was. Providing the exact commands issued and the resulting error will help me troubleshoot this with you. Let's see if we can get it figured out. On ubuntu, conda should be available in the standard terminal, so we will use that to install and run pingmapper. You will know that this is the case if you open the terminal and see Now proceed with Step 3. If the gdal error you previously reported persists, look to see if the line below is in the error: If it is, try installing wheel with: Then try install the pingmapper environment. Let me know how it goes! If you run into issues, please report the exact command and the resulting error. If the error is too long, please attach as txt. |
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Cameron,
Will do and let you know how it goes. I will get back to it in the next day
or so and will alot more time to both document and troubleshoot the issues.
Thanks for your time.
Mark
…On Mon, Jan 29, 2024 at 11:47 AM Cameron Bodine ***@***.***> wrote:
Thanks for the report and sorry that you are having issues. Note that I do
most of the development and testing of PING-Mapper on Ubuntu, so I can
confirm that it does work.
I confess I am a bit confused about your troubleshooting steps. It seems
you had to bounce around and tried a few things and it is not clear what
caused an error and what the error was. Providing the exact commands issued
and the resulting error will help me troubleshoot this with you. Let's see
if we can get it figured out.
There seems to be something off with your Anaconda install. Open your
terminal and update conda. On ubuntu, conda should be available in the
standard terminal. You will know that this is the case if you open the
terminal and see (base) before your username and current directory.
Now use the terminal to navigate to the location where you want to install
pingmapper. This must be a directory where you have write permissions.
Now proceed with Step 3
<https://cameronbodine.github.io/PINGMapper/docs/gettingstarted/Installation.html#step-3>
.
If the gdal error you previously reported persists, look to see if the
line below is in the error:
Using legacy 'setup.py install' for GDAL, since package 'wheel' is not installed.
If it is, try installing wheel with:
conda install conda-forge::wheel
Then try install the pingmapper environment. Let me know how it goes! If
you run into issues, please report the exact command and the resulting
error. If the error is too long, please attach as txt.
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In my attempts to fix my installation I decided to just start over from scratch. Downloaded newest version from Anaconda --> Anaconda3-2023.09-0-Linux-x86_64.sh initiated install via bash command: ---> bash Anaconda3-2023.09-0-Linux-x86_64.sh installation finished. #conda config --set auto_activate_base false You can undo this by running So installed over and in a directory I have full control over. Upon sourcing bash I got base activated #source ~/.bashrc (base) sidhatha@siddharthaX1:~/sonar2$ conda list shows packages: #conda list packages in environment at /home/siddhartha/anaconda3:Name Version Build Channel_anaconda_depends 2023.09 py311_mkl_1 Now to make directory as stated in directions from site: #mkdir PythonPackages Move into that directory Directions state to update conda and i will do so even though I just downloaded the newest version from Anaconda site #(base) sidhatha@siddharthaX1:~/anaconda3/PythonPackages$ conda update -n base conda system wants to downgrade a package? The following packages will be DOWNGRADED: scikit-learn 1.3.0-py311ha02d727_0 --> 1.2.2-py311h6a678d5_1 Going to skip that for now. Next item on install list in to install the conda-libmamba-solver (step 4) --> note in base to do so as in the example. #(base) sidhatha@siddharthaX1:~/anaconda3/PythonPackages$ conda install -n base conda-libmamba-solver Different response than before when attempting to install ;-} Collecting package metadata (current_repodata.json): done ==> WARNING: A newer version of conda exists. <== Please update conda by running Or to minimize the number of packages updated during conda update use Package Planenvironment location: /home/siddhartha/anaconda3 added / updated specs: The following packages will be downloaded: The following packages will be UPDATED: ca-certificates 2023.08.22-h06a4308_0 --> 2023.12.12-h06a4308_0 Proceed ([y]/n)? Downloading and Extracting Packages Preparing transaction: done Next direction is to set libmamba as default solver conda config --set solver libmamba --> from directions: (base) sidhatha@siddharthaX1:~/anaconda3/PythonPackages$ conda config --set solver libmamba response cleared Step 5 make sure git is installed --> assuming this is for conda itself as we have git installed via OS conda install git --> response below Channels:
Package Planenvironment location: /home/siddhartha/anaconda3 added / updated specs: The following packages will be downloaded: The following NEW packages will be INSTALLED: gdbm pkgs/main/linux-64::gdbm-1.18-hd4cb3f1_4 Proceed ([y]/n)? y Downloading and Extracting Packages Preparing transaction: done Step 6 clone PINGMapper git clone --depth 1 https://github.com/CameronBodine/PINGMapper --> note in base still (base) sidhatha@siddharthaX1:~/anaconda3/PythonPackages$ git clone --depth 1 https://github.com/CameronBodine/PINGMapper Cloning into 'PINGMapper'... more into PINGMapper directory cd PINGMapper Step 8: Create ping environment: (base) sidhatha@siddharthaX1:~/anaconda3/PythonPackages/PINGMapper$ conda env create --file conda/PINGMapper.yml Response: Channels:
Downloading and Extracting Packages done To activate this environment, use$ conda activate pingTo deactivate an active environment, use$ conda deactivatenow to activate the environment: conda activate ping response cleared --> now in the ping environment (ping) sidhatha@siddharthaX1:~/anaconda3/PythonPackages/PINGMapper$ Will move on to test and report Thx! |
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Test occurred but did get an error: test results--> Version: 2.15.0 Downloaded and extracted ./exampleData/Test_Small_DS.zip User Parameters ===========================================***** READING ***** Downloading segmentation models (v1.0): Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 6.2 | 26.2 | 2.9 Getting DAT Metadata... Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 1.3 | 26.2 | 2.9 Getting Header Structure... Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.3 | 26.2 | 2.9 Getting SON file header metadata... Locating missing pings and adding NoData... Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.2 | 33.1 | 4.1 Summary of Ping Metadata: B000 : ds_lowfreq Attribute | Minimum | Maximum | Average | Valid record_num | 3 | 13762 | 6882.008 | True B001 : ds_highfreq Attribute | Minimum | Maximum | Average | Valid record_num | 0 | 13763 | 6882.9 | True B002 : ss_port Attribute | Minimum | Maximum | Average | Valid record_num | 1 | 13760 | 6880.003 | True B003 : ss_star Attribute | Minimum | Maximum | Average | Valid record_num | 2 | 13761 | 6881.089 | True Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 33.1 | 4.1 Automatically estimating depth for 7 chunks: [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 7.5 | 27.2 | 3.0 Exporting bedpick plots to .jpg... Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 2.3 | 41.4 | 5.3 Automatically detecting shadows for 7 chunks: Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 8.7 | 30.9 | 3.7 Performing empirical gain normalization (EGN) on sonar intensities: [Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers. [Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers. Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 31.4 | 3.8 [Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers. [Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers. Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 32.4 | 3.9 [Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers. [Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers. MinMax Global Stretch Vals Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 1.0 | 32.6 | 4.0 Exporting sonogram tiles: [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.2 | 33.3 | 4.1 [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.5 | 35.6 | 4.5 Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 35.7 | 4.5 ===========================================***** RECTIFYING ***** Smoothing trackline... Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.2 | 35.7 | 4.5 Calculating, smoothing, and interpolating range extent coordinates... Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 28.7 | 3.3 Rectifying and exporting GeoTiffs: [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.7 | 32.8 | 4.0 [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 34.5 | 4.3 Done! Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.2 | 34.5 | 4.3 Mosaicing GeoTiffs... Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 34.7 | 4.3 Exporting Banklines... [Parallel(n_jobs=2)]: Using backend LokyBackend with 2 concurrent workers. Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 32.4 | 3.9 Current CPU/RAM Usage: CPU % | RAM % | RAM [GB] 0.0 | 32.4 | 3.9 ===========================================***** MAPPING SUBSTRATE ***** Using existing smoothed trackline. Automatically predicting and segmenting substrate... [Parallel(n_jobs=7)]: Using backend LokyBackend with 7 concurrent workers. !!!!!!!!!!!!!!!!! |
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Error log attached |
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Excellent! Though it did not finish, it appears everything installed correctly. Thank you for working through this! The problem now lies with a memory error. It is an issue with PINGMappers workflows. I will investigate for memory leaks and report back. |
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KK no worries it does appear to be working now and I am running the larger
test just to see the results. Next is to get some of my own equipment todo
mapping in the Chesapeake bay. I may ping you for some recommendations if
you don’t mind.
Regards and thx,
Mark
…On Tue, Jan 30, 2024 at 10:58 PM Cameron Bodine ***@***.***> wrote:
Excellent! Though it did not finish, it appears everything installed
correctly. Thank you for working through this!
The problem now lies with a memory error. It is an issue with PINGMappers
workflows. I will investigate for memory leaks and report back.
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Question? Is it possible to export an environment to pass on to another
person or system?
Mark
On Tue, Jan 30, 2024 at 11:15 PM Mark McIntosh ***@***.***>
wrote:
… KK no worries it does appear to be working now and I am running the larger
test just to see the results. Next is to get some of my own equipment todo
mapping in the Chesapeake bay. I may ping you for some recommendations if
you don’t mind.
Regards and thx,
Mark
On Tue, Jan 30, 2024 at 10:58 PM Cameron Bodine ***@***.***>
wrote:
> Excellent! Though it did not finish, it appears everything installed
> correctly. Thank you for working through this!
>
> The problem now lies with a memory error. It is an issue with PINGMappers
> workflows. I will investigate for memory leaks and report back.
>
> —
> Reply to this email directly, view it on GitHub
> <#111 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAGK3KY7NYN6CHHB7O3XCQTYRG6QHAVCNFSM6AAAAABCK46UBOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJYGMZTQMBXGU>
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> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
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Glad to hear you are up and running!
I am not sure, but I would not recommend this. It is better to build a conda environment on each system as the solver will take the new systems settings/configuration into account. I realize the install is a bit tedious, but it will be less so now that you have been through it and provided excellent documentation. Closing as complete! For my own notes:
This may be due to downloading SegFormer model, not a memory error. Needs further investigation. |
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Going to go ahead and run the longer test to see if it errors as well or passes. ----> it also erred out but a different manor: Error Thrown: The exit codes of the workers are {SIGKILL(-9)} |
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Sorry I did not notice this was closed and that is just fine once again thanks for the encouragement and assistance. |
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Looks like you have 12 gb of ram? IYou could try passing a -2 or -4 to the Thread Count ( |
Can this project be installed in a linux distro (Ubuntu?)
TIA
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