PALM - Historial de revisiones

Guido.tiscornia: /* Hydra, for this purpose */

2026-10-01T19:32:45Z

Hydra, for this purpose

← Revisión anterior		Revisión del 19:32 1 oct 2026
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	The Intel compiler was not used. Hydra’s Intel environment has two oneAPI installations (2021.4.0 with <code>ifort</code> and 2026.0 with <code>ifx</code>), and the MPICH <code>mpif90</code> calls an <code>ifort</code> that is not in the PATH. With a couple of patches a simple MPI “hello world” worked, but the PALM installer ended up producing a mixed build that failed at runtime with <code>undefined symbol: __netcdf_MOD_nf90_put_var...</code>. After two attempts we switched to a pure gfortran build.		The Intel compiler was not used. Hydra’s Intel environment has two oneAPI installations (2021.4.0 with <code>ifort</code> and 2026.0 with <code>ifx</code>), and the MPICH <code>mpif90</code> calls an <code>ifort</code> that is not in the PATH. With a couple of patches a simple MPI “hello world” worked, but the PALM installer ended up producing a mixed build that failed at runtime with <code>undefined symbol: __netcdf_MOD_nf90_put_var...</code>. After two attempts we switched to a pure gfortran build.

	== Hydra~~, for this purpose~~ ==		== Hydra==

	There is a single queue, <code>larga</code>. The nodes (as of July 2026; check with <code>pbsnodes</code>):		There is a single queue, <code>larga</code>. The nodes (as of July 2026; check with <code>pbsnodes</code>):

Guido.tiscornia: /* Tools and links */

2026-10-01T19:01:49Z

Tools and links

← Revisión anterior		Revisión del 19:01 1 oct 2026
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	== Tools and links ==		== Tools and links ==

	* GEO4PALM, to build the static driver from global datasets. Its code needs patches to work with current libraries: use Miniforge/conda-forge, numpy below 2, and <code>pip --extra-index-url</code> (not <code>-i</code>). https://github.com/dongqi-DQ/GEO4PALM (confirm the exact URL from the WRF4PALM README).
	* WRF4PALM, to build the dynamic driver from WRF output: https://github.com/dongqi-DQ/WRF4PALM
	* <code>palm_csd</code> (ships with PALM), <code>palmtest</code> and <code>palmplot</code>.
	* <code>ncview</code> and Python (xarray, netCDF4, matplotlib with the <code>Agg</code> backend) for looking at outputs. Pre- and post-processing were done on local machines.

	Documentation and downloads:		Documentation and downloads:
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	* https://gitlab.palm-model.org/releases/palm_model_system		* https://gitlab.palm-model.org/releases/palm_model_system
	* Maronga et al. 2020, PALM 6.0 overview: https://gmd.copernicus.org/articles/13/1335/2020/		* Maronga et al. 2020, PALM 6.0 overview: https://gmd.copernicus.org/articles/13/1335/2020/
	* Lin et al. 2021, WRF4PALM: https://doi.org/10.5194/gmd-14-2503-2021
	* Lin et al. 2024, GEO4PALM: https://doi.org/10.5194/gmd-17-815-2024

Guido.tiscornia: /* Pending */

2026-10-01T19:01:26Z

Pending

← Revisión anterior		Revisión del 19:01 1 oct 2026
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	</pre>		</pre>
	The <code>env LD_LIBRARY_PATH=</code> prefix is needed on Hydra because the system <code>ncdump</code> clashes with the NetCDF library that PALM’s environment puts first (<code>undefined symbol: nc_reclaim_data</code>). Output files get a suffix <code>.000</code>, <code>.001</code>, … per successful run. The <code>_cpu.NNN</code> file is only written if the run finished normally, so it is a good way to confirm it reached the end. Always look at the actual contents (<code>ls</code>, <code>ncdump -h</code>) before considering a run good.		The <code>env LD_LIBRARY_PATH=</code> prefix is needed on Hydra because the system <code>ncdump</code> clashes with the NetCDF library that PALM’s environment puts first (<code>undefined symbol: nc_reclaim_data</code>). Output files get a suffix <code>.000</code>, <code>.001</code>, … per successful run. The <code>_cpu.NNN</code> file is only written if the run finished normally, so it is a good way to confirm it reached the end. Always look at the actual contents (<code>ls</code>, <code>ncdump -h</code>) before considering a run good.

	~~== Pending ==~~

	* Test restart in batch (it failed in local interactive mode, because of the <code>palmrun</code> script and not PALM).
	* Scaling sweep with 96 and 128 processes inside a single node, and the multigrid solver.
	* Nested domains and a real dynamic driver (WRF4PALM) on Hydra.
	* Tell the administrators about the double oneAPI installation; there is no record that it has been fixed.

	== Tools and links ==		== Tools and links ==

Guido.tiscornia: /* Performance */

2026-10-01T19:00:14Z

Performance

@@ Línea 174: / Línea 174: @@
 </pre>
 The <code>env LD_LIBRARY_PATH=</code> prefix is needed on Hydra because the system <code>ncdump</code> clashes with the NetCDF library that PALM’s environment puts first (<code>undefined symbol: nc_reclaim_data</code>). Output files get a suffix <code>.000</code>, <code>.001</code>, … per successful run. The <code>_cpu.NNN</code> file is only written if the run finished normally, so it is a good way to confirm it reached the end. Always look at the actual contents (<code>ls</code>, <code>ncdump -h</code>) before considering a run good.
 == Pending ==

Guido.tiscornia: /* Setting up a case */

2026-10-01T18:59:05Z

Setting up a case

← Revisión anterior		Revisión del 18:59 1 oct 2026
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	* Only <code>_p3d</code> and <code>_static</code> files go in <code>INPUT/</code>. A backup there (for example <code>case_p3d.bak</code>) makes the run abort with <code>wrong ending</code>.		* Only <code>_p3d</code> and <code>_static</code> files go in <code>INPUT/</code>. A backup there (for example <code>case_p3d.bak</code>) makes the run abort with <code>wrong ending</code>.
	* <code>nx+1</code> and <code>ny+1</code> must factorize into 2, 3 and 5 ~~(Temperton FFT)~~. That is why 384 was used and not 400.		* <code>nx+1</code> and <code>ny+1</code> must factorize into 2, 3 and 5. That is why 384 was used and not 400.
	* PALM counts the maximum index (<code>nx = 383</code> means 384 points), while GEO4PALM counts points. If they do not match, the error is <code>static driver: horizontal dimension ... does not match model dimension</code>.		* PALM counts the maximum index (<code>nx = 383</code> means 384 points), while GEO4PALM counts points. If they do not match, the error is <code>static driver: horizontal dimension ... does not match model dimension</code>.
	* Always set <code>data_output_2d_on_each_pe = .FALSE.</code> in <code>&runtime_parameters</code>. With the default value, <code>combine_plot_fields</code> breaks on NFS and outputs are lost.		* Always set <code>data_output_2d_on_each_pe = .FALSE.</code> in <code>&runtime_parameters</code>. With the default value, <code>combine_plot_fields</code> breaks on NFS and outputs are lost.
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	/		/
	</pre>		</pre>

	== Monitoring and results ==		== Monitoring and results ==

Guido.tiscornia: /* Build */

2026-10-01T18:56:38Z

Build

← Revisión anterior		Revisión del 18:56 1 oct 2026
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	bash install -p ~/salidas/palm -s /usr -t /usr -x		bash install -p ~/salidas/palm -s /usr -t /usr -x
	</pre>		</pre>
	<code>-p</code> is the install prefix, <code>-s</code> and <code>-t</code> force the system NetCDF (otherwise autodetection picks Intel’s), and <code>-x</code> cleans the previous build. When it finishes, the executables are in <code>~/salidas/palm/bin</code> and the default configuration is <code>~/salidas/palm/.palm.config.default</code>. RRTMG is linked in~~. Parallel NetCDF is not available on Hydra, but this does not matter much: the computation is parallel and only the file writing is serial~~.		<code>-p</code> is the install prefix, <code>-s</code> and <code>-t</code> force the system NetCDF (otherwise autodetection picks Intel’s), and <code>-x</code> cleans the previous build. When it finishes, the executables are in <code>~/salidas/palm/bin</code> and the default configuration is <code>~/salidas/palm/.palm.config.default</code>. RRTMG is linked in.

	=== Interactive test ===		=== Interactive test ===

Guido.tiscornia: /* Environment script */

2026-10-01T18:56:00Z

Environment script

← Revisión anterior		Revisión del 18:56 1 oct 2026
Línea 61:		Línea 61:
	</pre>		</pre>
	It has to be sourced in every new terminal. After loading it, the second line must say <code>gfortran</code>; if it does not, do not continue.		It has to be sourced in every new terminal. After loading it, the second line must say <code>gfortran</code>; if it does not, do not continue.

	A practical tip: do not create the file by pasting a long <code>cat > file << EOF</code> block into the SSH terminal. Lines can get mixed up and the file ends up broken without it being obvious. Use <code>nano</code>/<code>vim</code>, or upload it with <code>scp</code>, and check it with <code>cat -n</code>.

	=== Build ===		=== Build ===

Guido.tiscornia: /* Installation */

2026-10-01T18:55:06Z

Installation

← Revisión anterior		Revisión del 18:55 1 oct 2026
Línea 23:		Línea 23:
	== Installation ==		== Installation ==

	Download (<code>git clone</code> asks for credentials, the tarball does not):		Download (at the moment <code>git clone</code> asks for credentials inside of PALM website, but the tarball does not):

	<pre>		<pre>

Guido.tiscornia: /* Environment script */

2026-10-01T18:54:13Z

Environment script

← Revisión anterior		Revisión del 18:54 1 oct 2026
Línea 33:		Línea 33:
	=== Environment script ===		=== Environment script ===

	Hydra’s default environment breaks PALM, so it has to be cleaned up. Save this as <code>~/cargar_entorno_palm.sh</code>:		Hydra’s default environment breaks PALM, so it has to be cleaned up. Save this, for example, as <code>~/cargar_entorno_palm.sh</code>:

	<pre>		<pre>

Guido.tiscornia: /* Hydra, for this purpose */

2026-10-01T18:53:01Z

Hydra, for this purpose

← Revisión anterior		Revisión del 18:53 1 oct 2026
Línea 20:		Línea 20:

	Memory is not requested from PBS: the whole node is allocated. Walltimes of up to 7 days are accepted without problems.		Memory is not requested from PBS: the whole node is allocated. Walltimes of up to 7 days are accepted without problems.

	~~<code>~/salidas</code> is an NFS mount and is the same location as <code>/nfsmounts/storage/scratch/<user></code>. PALM was installed there, in <code>~/salidas/palm</code>.~~

	== Installation ==		== Installation ==