CESMInstall WIKI CESM - hydra - Historial de revisiones

Lluis.fita: /* hydra's compilation environment */

2024-05-17T20:39:44Z

hydra's compilation environment

← Revisión anterior		Revisión del 20:39 17 may 2024
Línea 1047:		Línea 1047:
	Running /home/lluis.fita/intel_env.csh		Running /home/lluis.fita/intel_env.csh
	/bin/sh: 1: Syntax error: Bad fd number		/bin/sh: 1: Syntax error: Bad fd number
			</PRE>

			whereas the execution of the shell from terminal does not give any error
			<PRE style="shell">
			$ /bin/sh /home/lluis.fita/intel_env.csh

	</PRE>		</PRE>

Lluis.fita: /* hydra's compilation environment */

2024-05-17T20:15:29Z

hydra's compilation environment

← Revisión anterior		Revisión del 20:15 17 may 2024
Línea 796:		Línea 796:
	(...)		(...)
	-------------------------------------------------------------------------		-------------------------------------------------------------------------
	run command is /opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1		run command is /opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >>
			cesm.log.$LID 2>&1
	tm_poll: got event 1 return 0		tm_poll: got event 1 return 0
	tm_poll: INIT nodes 1		tm_poll: INIT nodes 1
Línea 804:		Línea 805:
	new_task: jobid=43629.hydra node=0 task=1		new_task: jobid=43629.hydra node=0 task=1
	new_task: jobid=43629.hydra node=0 task=2		new_task: jobid=43629.hydra node=0 task=2
	ERROR: RUN FAIL: Command '/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/~~cesm~~.exe >> cesm.log.$LID 2>&1 ' failed		ERROR: RUN FAIL: Command '/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/ces
			m.exe >> cesm.log.$LID 2>&1 ' failed
	See log file for details: /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43629.hydra.240516-170533		See log file for details: /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43629.hydra.240516-170533

Línea 1021:		Línea 1023:
	Creation of a simple shell script with the required content in <CODE>/home/lluis.fita/intel_env.csh</CODE>		Creation of a simple shell script with the required content in <CODE>/home/lluis.fita/intel_env.csh</CODE>
	<PRE>		<PRE>
	#!/bin/~~csh~~		#!/bin/sh
	export PATH="/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin:$PATH"		export PATH="/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin:$PATH"
	export PATH="/opt/netcdf/netcdf-4/intel/2021.4.0/bin:$PATH"		export PATH="/opt/netcdf/netcdf-4/intel/2021.4.0/bin:$PATH"
Línea 1039:		Línea 1041:
	<desc>External script to be run before model completion</desc>		<desc>External script to be run before model completion</desc>
	<values>		<values>
	<value>/home/lluis/intel_env.~~csh~~</value>		<value>/home/lluis/intel_env.sh</value>
	</values>		</values>
	$ ./case.submit		$ ./case.submit
	$ cat run.b.day1.0.~~o43641~~		$ cat run.b.day1.0.o43647
	~~ERROR: External script 'source~~ /~~opt~~/~~load-libs~~.sh 1~~' not found~~		Running /home/lluis.fita/intel_env.csh
			/bin/sh: 1: Syntax error: Bad fd number
	</PRE>		</PRE>

Lluis.fita: /* hydra's compilation environment */

2024-05-17T20:04:12Z

hydra's compilation environment

@@ Línea 978: / Línea 978: @@
 </PRE>
-Is set to use the variable <CODE>prerun_script</CODE> into the file in the case directory <CODE>env_run.xml</CODE>, see more details looking for it [https://docs.cesm.ucar.edu/models/cesm2/settings/current/drv_input.html here]
+Is set to use the variable <CODE>prerun_script</CODE> into the file in the case directory <CODE>env_run.xml</CODE>, see more details (searching for it [https://docs.cesm.ucar.edu/models/cesm2/settings/current/drv_input.html here])
 Trying different options:
@@ Línea 1013: / Línea 1013: @@
        <values>
          <value>'source /opt/load-libs.sh 1'</value>
        </values>
 $ ./case.submit

Lluis.fita: /* hydra's compilation environment */

2024-05-17T19:34:29Z

hydra's compilation environment

← Revisión anterior		Revisión del 19:34 17 may 2024
Línea 979:		Línea 979:

	Is set to use the variable <CODE>prerun_script</CODE> into the file in the case directory <CODE>env_run.xml</CODE>, see more details looking for it [https://docs.cesm.ucar.edu/models/cesm2/settings/current/drv_input.html here]		Is set to use the variable <CODE>prerun_script</CODE> into the file in the case directory <CODE>env_run.xml</CODE>, see more details looking for it [https://docs.cesm.ucar.edu/models/cesm2/settings/current/drv_input.html here]

			Trying different options:
	<PRE>		<PRE>
	<entry id="PRERUN_SCRIPT">		<entry id="PRERUN_SCRIPT">
Línea 991:		Línea 993:
	</PRE>		</PRE>

			Looking inside /opt/load-libs.sh
	<PRE>		<PRE>
	<entry id="PRERUN_SCRIPT">		<entry id="PRERUN_SCRIPT">
Línea 1002:		Línea 1005:
	Running /opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh		Running /opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh
	/bin/sh: 1: Syntax error: Bad fd number		/bin/sh: 1: Syntax error: Bad fd number
			</PRE>

			<PRE>
			<entry id="PRERUN_SCRIPT">
			<type>char</type>
			<desc>External script to be run before model completion</desc>
			<values>
			<value>'source /opt/load-libs.sh 1'</value>
			</values>
			$ ./case.submit
			$ cat run.b.day1.0.o43641
			ERROR: External script 'source /opt/load-libs.sh 1' not found
	</PRE>		</PRE>

Lluis.fita: /* Errors */

2024-05-17T19:14:11Z

Errors

← Revisión anterior		Revisión del 19:14 17 may 2024
Línea 755:		Línea 755:

	=== Errors ===		=== Errors ===

			==== mpirun not found ====

	Submission error as:		Submission error as:
	<PRE style="shell">		<PRE style="shell">
Línea 771:		Línea 774:
	</PRE>		</PRE>
	If it is too late (prior to submit), it can be directly changed in the case directory in file <CODE>env_mach_specific.xml</CODE>		If it is too late (prior to submit), it can be directly changed in the case directory in file <CODE>env_mach_specific.xml</CODE>

			==== hydra's compilation environment ====

	Simulation finished too early ...		Simulation finished too early ...

Lluis.fita: /* Errors */

2024-05-17T19:13:07Z

Errors

@@ Línea 971: / Línea 971: @@
 h file or directory
 (...)
 </PRE>

Lluis.fita: /* Errors */

2024-05-17T18:59:23Z

Errors

← Revisión anterior		Revisión del 18:59 17 may 2024
Línea 950:		Línea 950:
	</PRE>		</PRE>

	I suspect that it is related to the compilation environment. hydra does not have <CODE>module</CODE>. It set-ups compilation environment via shell scriupt <CODE>/opt/load-libs.sh</CODE>. There must be a way to systematically introduce it in the <CODE>config_batch.xml</CODE> in order to be executed in all the PBS jobs.		I suspect that it is related to the compilation environment. hydra does not have <CODE>module</CODE>. It set-ups compilation environment via shell scriupt <CODE>/opt/load-libs.sh</CODE>. There must be a way to systematically introduce it in the <CODE>config_batch.xml</CODE> in order to be executed in all the PBS jobs. A new post is created in the CESM forum [https://bb.cgd.ucar.edu/cesm/threads/introducing-a-system-instruction-in-config_batch-xml.9646/#post-55530 #post-55530]

			From another attempt
	<PRE style="shell">		<PRE style="shell">
			$ cat /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43633.hydra.240517-155125 \| more
			/home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading
			shared libraries: libnetcdf.so.19: cannot open shared object file: No suc
			h file or directory
			/home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading
			shared libraries: libnetcdf.so.19: cannot open shared object file: No suc
			h file or directory
			/home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading
			shared libraries: libnetcdf.so.19: cannot open shared object file: No suc
			h file or directory
			/home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading
			shared libraries: libnetcdf.so.19: cannot open shared object file: No suc
			h file or directory
			/home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading
			shared libraries: libnetcdf.so.19: cannot open shared object file: No suc
			h file or directory
			(...)
	</PRE>		</PRE>

Lluis.fita en 20:30 16 may 2024

2024-05-16T20:30:48Z

← Revisión anterior		Revisión del 20:30 16 may 2024
Línea 1:		Línea 1:
	These are the CESM's installation notes in [http://www.cima.fcen.uba.ar/ CIMA]/[http://www.cima.fcen.uba.ar/UMI/ IFAECI]'s HPC called <CODE>hydra</CODE>.		These are the CESM's installation notes in [http://www.cima.fcen.uba.ar/ CIMA]/[http://www.cima.fcen.uba.ar/UMI/ IFAECI]'s HPC called <CODE>hydra</CODE>.

	Notes and process carried out on 13-17th of May 2024, by Lluís Fita (UBA/CIMA/IFAECI, CABA, Argentina) with the assistance of Ass. Prof. Pedro DiNezio (U. Colorado, Boulder) and Dr Nicolás J. Cosentino (UBA/CIMA/IFAECI, CABA, Argentina), and the non-anonymous help of ~~stackoveflow,~~ CESM forum and ~~posts.~~		Notes and process carried out on 13-17th of May 2024, by Lluís Fita (UBA/CIMA/IFAECI, CABA, Argentina) with the assistance of Ass. Prof. Pedro DiNezio (U. Colorado, Boulder) and Dr Nicolás J. Cosentino (UBA/CIMA/IFAECI, CABA, Argentina), and the non-anonymous help of [https://bb.cgd.ucar.edu/cesm/ CESM forum] and stackoverflow

	= intel compilation =		= intel compilation =

Lluis.fita en 20:29 16 may 2024

2024-05-16T20:29:32Z

← Revisión anterior		Revisión del 20:29 16 may 2024
Línea 1:		Línea 1:
	These are the CESM's installation notes in [CIMA]/[IFAECI]'s HPC called <CODE>hydra</CODE>.		These are the CESM's installation notes in [http://www.cima.fcen.uba.ar/ CIMA]/[http://www.cima.fcen.uba.ar/UMI/ IFAECI]'s HPC called <CODE>hydra</CODE>.

	Notes and process carried out on 13-17th of May 2024, by Lluís Fita (CIMA/IFAECI, CABA, Argentina) with the assistance of Ass. Prof. Pedro DiNezio (U. Colorado, Boulder) and Dr Nicolás J. Cosentino (CIMA/IFAECI, CABA, Argentina), and the non-anonymous help of stackoveflow, CESM forum and posts.		Notes and process carried out on 13-17th of May 2024, by Lluís Fita (UBA/CIMA/IFAECI, CABA, Argentina) with the assistance of Ass. Prof. Pedro DiNezio (U. Colorado, Boulder) and Dr Nicolás J. Cosentino (UBA/CIMA/IFAECI, CABA, Argentina), and the non-anonymous help of stackoveflow, CESM forum and posts.

	= intel compilation =		= intel compilation =

Lluis.fita en 20:28 16 may 2024

2024-05-16T20:28:31Z

← Revisión anterior		Revisión del 20:28 16 may 2024
Línea 1:		Línea 1:
			These are the CESM's installation notes in [CIMA]/[IFAECI]'s HPC called <CODE>hydra</CODE>.

			Notes and process carried out on 13-17th of May 2024, by Lluís Fita (CIMA/IFAECI, CABA, Argentina) with the assistance of Ass. Prof. Pedro DiNezio (U. Colorado, Boulder) and Dr Nicolás J. Cosentino (CIMA/IFAECI, CABA, Argentina), and the non-anonymous help of stackoveflow, CESM forum and posts.

	= intel compilation =		= intel compilation =