CCLM in levante at DKRZ – in #9: CCLM

in #9: CCLM

<p> Hi Community, </p> <p> has anybody started running <span class="caps"> CCLM </span> on the new machine at <span class="caps"> DKRZ </span> , the levante? <br/> Could you share your Fopts files? </p> <p> Cheers, <br/> Bijan </p>

  @bijanhassanabadifallah in #9f0ba82

<p> Hi Community, </p> <p> has anybody started running <span class="caps"> CCLM </span> on the new machine at <span class="caps"> DKRZ </span> , the levante? <br/> Could you share your Fopts files? </p> <p> Cheers, <br/> Bijan </p>

CCLM in levante at DKRZ

BF wrote

Hi Community,

has anybody started running CCLM on the new machine at DKRZ , the levante?
Could you share your Fopts files?

Cheers,
Bijan

View in channel
<p> For those who are interested, I used the following setting to install int2lm and cclm on Levante. <br/> “Note that the paths can change because <span class="caps"> DKRZ </span> is still recreating the entire software tree. <br/> It should become more stable in the near future”. The cdo and nco are not installed yet but will be soon there. </p> <p> <span class="caps"> NETCDFC </span> _ROOT = /sw/spack-levante/netcdf-c-4.8.1-qk24yp <br/> NETCDFF_ROOT = /sw/spack-levante/netcdf-fortran-4.5.3-k6xq5g <br/> HDF5_ROOT = /sw/spack-levante/hdf5-1.12.1-akf2kp <br/> SZIP_ROOT = /sw/spack-levante/libaec-1.0.5-r5sdw5 </p> <p> and change the following line in Fopts: </p> <p> <strong> NC_LIB += -L$( <span class="caps"> SZIP </span> _ROOT)/lib -lsz -lm </strong> </p> <p> to </p> <p> <strong> NC_LIB += -L$( <span class="caps"> SZIP </span> _ROOT)/lib64 -lsz -lm </strong> </p> <p> Cheers, <br/> Bijan </p>

  @bijanhassanabadifallah in #70c9dda

<p> For those who are interested, I used the following setting to install int2lm and cclm on Levante. <br/> “Note that the paths can change because <span class="caps"> DKRZ </span> is still recreating the entire software tree. <br/> It should become more stable in the near future”. The cdo and nco are not installed yet but will be soon there. </p> <p> <span class="caps"> NETCDFC </span> _ROOT = /sw/spack-levante/netcdf-c-4.8.1-qk24yp <br/> NETCDFF_ROOT = /sw/spack-levante/netcdf-fortran-4.5.3-k6xq5g <br/> HDF5_ROOT = /sw/spack-levante/hdf5-1.12.1-akf2kp <br/> SZIP_ROOT = /sw/spack-levante/libaec-1.0.5-r5sdw5 </p> <p> and change the following line in Fopts: </p> <p> <strong> NC_LIB += -L$( <span class="caps"> SZIP </span> _ROOT)/lib -lsz -lm </strong> </p> <p> to </p> <p> <strong> NC_LIB += -L$( <span class="caps"> SZIP </span> _ROOT)/lib64 -lsz -lm </strong> </p> <p> Cheers, <br/> Bijan </p>
BF replied

For those who are interested, I used the following setting to install int2lm and cclm on Levante.
“Note that the paths can change because DKRZ is still recreating the entire software tree.
It should become more stable in the near future”. The cdo and nco are not installed yet but will be soon there.

NETCDFC _ROOT = /sw/spack-levante/netcdf-c-4.8.1-qk24yp
NETCDFF_ROOT = /sw/spack-levante/netcdf-fortran-4.5.3-k6xq5g
HDF5_ROOT = /sw/spack-levante/hdf5-1.12.1-akf2kp
SZIP_ROOT = /sw/spack-levante/libaec-1.0.5-r5sdw5

and change the following line in Fopts:

NC_LIB += -L$( SZIP _ROOT)/lib -lsz -lm

to

NC_LIB += -L$( SZIP _ROOT)/lib64 -lsz -lm

Cheers,
Bijan

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<p> Thanks! This looks promising. <br/> What modules do you load? <br/> Can you attach the whole Fopts, please? </p>

  @burkhardtrockel in #e221fdf

<p> Thanks! This looks promising. <br/> What modules do you load? <br/> Can you attach the whole Fopts, please? </p>
BR replied

Thanks! This looks promising.
What modules do you load?
Can you attach the whole Fopts, please?

View in channel
<p> I tried the libraries, they work fine. <br/> But which modules did you load? <br/> I compiled int2lm using mpif90, but I can’t run it since modules like “mxm” are not yet installed. </p> <p> Thank you for helping. <br/> Mostafa </p>

  @mostafahamouda in #1fde949

<p> I tried the libraries, they work fine. <br/> But which modules did you load? <br/> I compiled int2lm using mpif90, but I can’t run it since modules like “mxm” are not yet installed. </p> <p> Thank you for helping. <br/> Mostafa </p>
MH replied

I tried the libraries, they work fine.
But which modules did you load?
I compiled int2lm using mpif90, but I can’t run it since modules like “mxm” are not yet installed.

Thank you for helping.
Mostafa

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<p> I have found the modules. It is fine now. </p>

  @burkhardtrockel in #32371ec

<p> I have found the modules. It is fine now. </p>
BR replied

I have found the modules. It is fine now.

View in channel
<p> Could you share them? <br/> Thank you </p>

  @mostafahamouda in #c9f5344

<p> Could you share them? <br/> Thank you </p>
MH replied

Could you share them?
Thank you

View in channel
<p> openmpi/4.1.2-intel-2021.5.0 <br/> intel-oneapi-compilers/2022.0.1-gcc-11.2.0 </p>

  @burkhardtrockel in #f95a6b5

<p> openmpi/4.1.2-intel-2021.5.0 <br/> intel-oneapi-compilers/2022.0.1-gcc-11.2.0 </p>
BR replied

openmpi/4.1.2-intel-2021.5.0
intel-oneapi-compilers/2022.0.1-gcc-11.2.0

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<p> Thank you. It compiled fine. However I still have problems with <span class="caps"> MPI </span> Runtime Settings. <br/> Could you share yours? </p> <p> I am getting an error such as: <br/> Caught signal 11 (Segmentation fault: address not mapped to object at address </p> <p> Thank you </p>

  @mostafahamouda in #9c55da4

<p> Thank you. It compiled fine. However I still have problems with <span class="caps"> MPI </span> Runtime Settings. <br/> Could you share yours? </p> <p> I am getting an error such as: <br/> Caught signal 11 (Segmentation fault: address not mapped to object at address </p> <p> Thank you </p>
MH replied

Thank you. It compiled fine. However I still have problems with MPI Runtime Settings.
Could you share yours?

I am getting an error such as:
Caught signal 11 (Segmentation fault: address not mapped to object at address

Thank you

View in channel
<p> Hi Community </p> <p> Thanks for the useful information, I successfully compiled the <span class="caps"> CCLM </span> and int2lm. But while I was trying to run the model, it gave me this error: <br/> sbatch: unrecognized option ‘—purge-slurm-env‘ <br/> Try “sbatch —help” for more information </p> <p> Does anyone know about this? it is because of the subchain script? Do we need to update the subchain script? </p> <p> Thank you very much in advance. </p> <p> Cheers <br/> Mingyue </p>

  @mingyuezhang in #19ae5a6

<p> Hi Community </p> <p> Thanks for the useful information, I successfully compiled the <span class="caps"> CCLM </span> and int2lm. But while I was trying to run the model, it gave me this error: <br/> sbatch: unrecognized option ‘—purge-slurm-env‘ <br/> Try “sbatch —help” for more information </p> <p> Does anyone know about this? it is because of the subchain script? Do we need to update the subchain script? </p> <p> Thank you very much in advance. </p> <p> Cheers <br/> Mingyue </p>
MZ replied

Hi Community

Thanks for the useful information, I successfully compiled the CCLM and int2lm. But while I was trying to run the model, it gave me this error:
sbatch: unrecognized option ‘—purge-slurm-env‘
Try “sbatch —help” for more information

Does anyone know about this? it is because of the subchain script? Do we need to update the subchain script?

Thank you very much in advance.

Cheers
Mingyue

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<p> Hi Mingyue, </p> <p> I commented that in int2lm code (i.e. removed that line) and got no errors. It is a slurm flag I think. <br/> Cheers, <br/> Bijan </p>

  @bijanhassanabadifallah in #2b4fbf2

<p> Hi Mingyue, </p> <p> I commented that in int2lm code (i.e. removed that line) and got no errors. It is a slurm flag I think. <br/> Cheers, <br/> Bijan </p>
BF replied

Hi Mingyue,

I commented that in int2lm code (i.e. removed that line) and got no errors. It is a slurm flag I think.
Cheers,
Bijan

View in channel
<p> Hi Bijan </p> <p> Thank you very much, I figured it out later I posted my confusion, but while running the model, it still gives errors such as “lib” missing, I think this is related to the Levante system build-up. </p> <p> Cheers <br/> Mingyue </p>

  @mingyuezhang in #c157e0f

<p> Hi Bijan </p> <p> Thank you very much, I figured it out later I posted my confusion, but while running the model, it still gives errors such as “lib” missing, I think this is related to the Levante system build-up. </p> <p> Cheers <br/> Mingyue </p>
MZ replied

Hi Bijan

Thank you very much, I figured it out later I posted my confusion, but while running the model, it still gives errors such as “lib” missing, I think this is related to the Levante system build-up.

Cheers
Mingyue

View in channel
<p> Hi, Community </p> <p> Thanks for the useful information, I successfully compiled the <span class="caps"> CCLM </span> and int2lm. Int2lm runs without any issues, but cclm stops with an error: <strong> —————————————————————————————— </strong> 0: * <span class="caps"> PROGRAM </span> <span class="caps"> TERMINATED </span> <span class="caps"> BECAUSE </span> OF <span class="caps"> ERRORS </span> DETECTED 0: * IN <span class="caps"> ROUTINE </span> : output_data 0: * 0: * <span class="caps"> ERROR </span> <span class="caps"> CODE </span> is 2035 0: * Error writing netcdf 2D variable 0: <strong> —————————————————————————————— </strong> </p> <p> I used <span class="caps"> COSMO </span> - <span class="caps"> CLM </span> v5.0, I want to ask is there anyone who experienced the same issue? or perhaps you have some idea on how to solve this problem? </p> <p> Thank you all very much in advance. <br/> Mingyue </p>

  @mingyuezhang in #e55d932

<p> Hi, Community </p> <p> Thanks for the useful information, I successfully compiled the <span class="caps"> CCLM </span> and int2lm. Int2lm runs without any issues, but cclm stops with an error: <strong> —————————————————————————————— </strong> 0: * <span class="caps"> PROGRAM </span> <span class="caps"> TERMINATED </span> <span class="caps"> BECAUSE </span> OF <span class="caps"> ERRORS </span> DETECTED 0: * IN <span class="caps"> ROUTINE </span> : output_data 0: * 0: * <span class="caps"> ERROR </span> <span class="caps"> CODE </span> is 2035 0: * Error writing netcdf 2D variable 0: <strong> —————————————————————————————— </strong> </p> <p> I used <span class="caps"> COSMO </span> - <span class="caps"> CLM </span> v5.0, I want to ask is there anyone who experienced the same issue? or perhaps you have some idea on how to solve this problem? </p> <p> Thank you all very much in advance. <br/> Mingyue </p>
MZ replied

Hi, Community

Thanks for the useful information, I successfully compiled the CCLM and int2lm. Int2lm runs without any issues, but cclm stops with an error: —————————————————————————————— 0: * PROGRAM TERMINATED BECAUSE OF ERRORS DETECTED 0: * IN ROUTINE : output_data 0: * 0: * ERROR CODE is 2035 0: * Error writing netcdf 2D variable 0: ——————————————————————————————

I used COSMO - CLM v5.0, I want to ask is there anyone who experienced the same issue? or perhaps you have some idea on how to solve this problem?

Thank you all very much in advance.
Mingyue

View in channel
<p> Two possibilites, dear Mingyue, </p> <p> A) There is a <span class="caps"> NETCDF </span> -library problem. Hopefully, you have used the compiler <span class="caps"> NETCDF </span> settings given by ‘nc-config —all’ </p> <p> B) There is a configuration problem. Maybe, you start with an output configuration where only one variable is written out in only one output stream. </p> <p> I am convinced that the error code is thrown out from the <span class="caps"> NETCDF </span> -Libraries and not the <span class="caps"> COSMO </span> model itself. </p> <p> Bye, <br/> Ronny </p>

  @ronnypetrik in #ea63878

<p> Two possibilites, dear Mingyue, </p> <p> A) There is a <span class="caps"> NETCDF </span> -library problem. Hopefully, you have used the compiler <span class="caps"> NETCDF </span> settings given by ‘nc-config —all’ </p> <p> B) There is a configuration problem. Maybe, you start with an output configuration where only one variable is written out in only one output stream. </p> <p> I am convinced that the error code is thrown out from the <span class="caps"> NETCDF </span> -Libraries and not the <span class="caps"> COSMO </span> model itself. </p> <p> Bye, <br/> Ronny </p>
RP replied

Two possibilites, dear Mingyue,

A) There is a NETCDF -library problem. Hopefully, you have used the compiler NETCDF settings given by ‘nc-config —all’

B) There is a configuration problem. Maybe, you start with an output configuration where only one variable is written out in only one output stream.

I am convinced that the error code is thrown out from the NETCDF -Libraries and not the COSMO model itself.

Bye,
Ronny

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<p> HI Ronny, </p> <p> Thanks for the quick reply. <br/> Unfortunately I do not remember that I have used or changed some line that contains the “nc-config —all” in any files. <br/> Perhaps you know where I should use this command? in the Fobts file or the general my home directory? </p> <p> Cheers <br/> Mingyue </p>

  @mingyuezhang in #4915478

<p> HI Ronny, </p> <p> Thanks for the quick reply. <br/> Unfortunately I do not remember that I have used or changed some line that contains the “nc-config —all” in any files. <br/> Perhaps you know where I should use this command? in the Fobts file or the general my home directory? </p> <p> Cheers <br/> Mingyue </p>
MZ replied

HI Ronny,

Thanks for the quick reply.
Unfortunately I do not remember that I have used or changed some line that contains the “nc-config —all” in any files.
Perhaps you know where I should use this command? in the Fobts file or the general my home directory?

Cheers
Mingyue

View in channel
<p> Hey Mingyue, </p> <p> first go for the option B). Throw away all output except for one variable and one output block. </p> <p> On which machine do you work? </p> <p> Bye, <br/> Ronny </p>

  @ronnypetrik in #4753204

<p> Hey Mingyue, </p> <p> first go for the option B). Throw away all output except for one variable and one output block. </p> <p> On which machine do you work? </p> <p> Bye, <br/> Ronny </p>
RP replied

Hey Mingyue,

first go for the option B). Throw away all output except for one variable and one output block.

On which machine do you work?

Bye,
Ronny

View in channel
<p> Hi Ronny </p> <p> I am on Levante. <br/> And what do you mean by “ Throw away all output except for one variable and one output block “? Sorry that I didn’t understand. </p> <p> Cheers <br/> Mingyue </p>

  @mingyuezhang in #e104f12

<p> Hi Ronny </p> <p> I am on Levante. <br/> And what do you mean by “ Throw away all output except for one variable and one output block “? Sorry that I didn’t understand. </p> <p> Cheers <br/> Mingyue </p>
MZ replied

Hi Ronny

I am on Levante.
And what do you mean by “ Throw away all output except for one variable and one output block “? Sorry that I didn’t understand.

Cheers
Mingyue

View in channel
<p> Hello Mingyue, </p> <p> I mean the namelist of <span class="caps"> COSMO </span> - <span class="caps"> CLM </span> </p> <p> <code> !!out01: &amp;GRIBOUT yform_write='ncdf', ncomb=${NSTART},${NNEXT},${NOUT_INC[$((NOUTDIR+=1))]}, yvarml='FRESHSNW','QV_S','T_S','T_SNOW','T_SO','W_I','W_SNOW','W_SO', 'PP','QC','QI','QR','QS','Z0','QV','T','U','V','W', !QG is only available in high-resolution runs yvarpl=' ', yvarzl=' ', luvmasspoint=.FALSE., lcheck = .FALSE., lwrite_const= ${LWRITE_CONST}, ydir='${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/', ytunit='d', /END </code> </p> <p> Throw away all variables in yvarml and leave only one. </p> <p> Bye, <br/> Ronny </p>

  @ronnypetrik in #4d271f6

<p> Hello Mingyue, </p> <p> I mean the namelist of <span class="caps"> COSMO </span> - <span class="caps"> CLM </span> </p> <p> <code> !!out01: &amp;GRIBOUT yform_write='ncdf', ncomb=${NSTART},${NNEXT},${NOUT_INC[$((NOUTDIR+=1))]}, yvarml='FRESHSNW','QV_S','T_S','T_SNOW','T_SO','W_I','W_SNOW','W_SO', 'PP','QC','QI','QR','QS','Z0','QV','T','U','V','W', !QG is only available in high-resolution runs yvarpl=' ', yvarzl=' ', luvmasspoint=.FALSE., lcheck = .FALSE., lwrite_const= ${LWRITE_CONST}, ydir='${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/', ytunit='d', /END </code> </p> <p> Throw away all variables in yvarml and leave only one. </p> <p> Bye, <br/> Ronny </p>
RP replied

Hello Mingyue,

I mean the namelist of COSMO - CLM

!!out01: &GRIBOUT yform_write='ncdf', ncomb=${NSTART},${NNEXT},${NOUT_INC[$((NOUTDIR+=1))]}, yvarml='FRESHSNW','QV_S','T_S','T_SNOW','T_SO','W_I','W_SNOW','W_SO', 'PP','QC','QI','QR','QS','Z0','QV','T','U','V','W', !QG is only available in high-resolution runs yvarpl=' ', yvarzl=' ', luvmasspoint=.FALSE., lcheck = .FALSE., lwrite_const= ${LWRITE_CONST}, ydir='${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/', ytunit='d', /END

Throw away all variables in yvarml and leave only one.

Bye,
Ronny

View in channel
<p> user#270 wrote: <br/> &gt; Hello Mingyue, <br/> &gt; <br/> &gt; I mean the namelist of COSMO-CLM <br/> &gt; <br/> &gt; <code> !!out01: &gt; &amp;GRIBOUT &gt; yform_write='ncdf', &gt; ncomb=${NSTART},${NNEXT},${NOUT_INC[$((NOUTDIR+=1))]}, &gt; yvarml='FRESHSNW','QV_S','T_S','T_SNOW','T_SO','W_I','W_SNOW','W_SO', &gt; 'PP','QC','QI','QR','QS','Z0','QV','T','U','V','W', !QG is only available in high-resolution runs &gt; yvarpl=' ', &gt; yvarzl=' ', &gt; luvmasspoint=.FALSE., &gt; lcheck = .FALSE., &gt; lwrite_const= ${LWRITE_CONST}, &gt; ydir='${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/', &gt; ytunit='d', &gt; /END &gt; </code> <br/> &gt; <br/> &gt; Throw away all variables in yvarml and leave only one. <br/> &gt; <br/> &gt; Bye, <br/> &gt; Ronny </p> <p> Hi, Ronny, </p> <p> I commented out all the output but ‘ <span class="caps"> FRESHSNW </span> ’ in output01, (all the variables from the other output channel are also commented out), like this &amp;GRIBOUT ! out01 yform_write=‘ncdf’, ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( <span class="caps"> NOUTDIR </span> +=1))]}, <br/> ! uncomment the next but one line if you plan double nesting yvarml=‘ <span class="caps"> FRESHSNW </span> ’, !‘QV_S’,‘T_S’,‘T_SNOW’,‘T_SO’,‘W_I’,‘W_SNOW’,‘W_SO’, !‘PP’,‘QC’,‘QI’,‘QR’,‘QS’,‘QV’,‘T’,‘U’,‘V’, yvarpl=’ ‘, yvarzl=’ ‘, luvmasspoint=.FALSE., lcheck = .FALSE., lwrite_const= ${LWRITE_CONST}, ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, ytunit=‘d’, /END <br/> ! &amp;GRIBOUT ! out02 <br/> ! yform_write=‘ncdf’, <br/> ! ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( <span class="caps"> NOUTDIR </span> +=1))]}, <br/> ! yvarml=‘W’,‘P’, <br/> ! yvarpl=’ ‘, <br/> ! yvarzl=’ ‘, <br/> ! luvmasspoint=.TRUE., <br/> ! lcheck = .FALSE., <br/> ! lwrite_const= ${LWRITE_CONST}, <br/> ! ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, <br/> ! ytunit=‘d’, <br/> ! /END <br/> ! &amp;GRIBOUT ! out03 <br/> ! yform_write=‘ncdf’, <br/> ! ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( <span class="caps"> NOUTDIR </span> +=1))]}, <br/> ! yvarml=‘ <span class="caps"> RAIN </span> _CON’,‘ <span class="caps"> SNOW </span> _CON’,‘ <span class="caps"> RAIN </span> _GSP’,‘ <span class="caps"> SNOW </span> _GSP’,‘ <span class="caps"> TOT </span> _PREC’, <br/> ! yvarpl=’ ‘, <br/> ! yvarzl=’ ‘, <br/> ! luvmasspoint=.TRUE., <br/> ! lcheck = .FALSE., <br/> ! lwrite_const= ${LWRITE_CONST}, ! ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, <br/> ! ytunit=‘d’, ! /END </p> <p> and then I got the following error: </p> <p> 137: <strong> —————————————————————————————— </strong> <br/> 137: * <span class="caps"> PROGRAM </span> <span class="caps"> TERMINATED </span> <span class="caps"> BECAUSE </span> OF <span class="caps"> ERRORS </span> DETECTED <br/> 137: * IN <span class="caps"> ROUTINE </span> : organize_data: input <br/> 138: <strong> —————————————————————————————— </strong> </p> <p> Cheers <br/> Mingyue </p>

  @mingyuezhang in #b03c5c5

<p> user#270 wrote: <br/> &gt; Hello Mingyue, <br/> &gt; <br/> &gt; I mean the namelist of COSMO-CLM <br/> &gt; <br/> &gt; <code> !!out01: &gt; &amp;GRIBOUT &gt; yform_write='ncdf', &gt; ncomb=${NSTART},${NNEXT},${NOUT_INC[$((NOUTDIR+=1))]}, &gt; yvarml='FRESHSNW','QV_S','T_S','T_SNOW','T_SO','W_I','W_SNOW','W_SO', &gt; 'PP','QC','QI','QR','QS','Z0','QV','T','U','V','W', !QG is only available in high-resolution runs &gt; yvarpl=' ', &gt; yvarzl=' ', &gt; luvmasspoint=.FALSE., &gt; lcheck = .FALSE., &gt; lwrite_const= ${LWRITE_CONST}, &gt; ydir='${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/', &gt; ytunit='d', &gt; /END &gt; </code> <br/> &gt; <br/> &gt; Throw away all variables in yvarml and leave only one. <br/> &gt; <br/> &gt; Bye, <br/> &gt; Ronny </p> <p> Hi, Ronny, </p> <p> I commented out all the output but ‘ <span class="caps"> FRESHSNW </span> ’ in output01, (all the variables from the other output channel are also commented out), like this &amp;GRIBOUT ! out01 yform_write=‘ncdf’, ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( <span class="caps"> NOUTDIR </span> +=1))]}, <br/> ! uncomment the next but one line if you plan double nesting yvarml=‘ <span class="caps"> FRESHSNW </span> ’, !‘QV_S’,‘T_S’,‘T_SNOW’,‘T_SO’,‘W_I’,‘W_SNOW’,‘W_SO’, !‘PP’,‘QC’,‘QI’,‘QR’,‘QS’,‘QV’,‘T’,‘U’,‘V’, yvarpl=’ ‘, yvarzl=’ ‘, luvmasspoint=.FALSE., lcheck = .FALSE., lwrite_const= ${LWRITE_CONST}, ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, ytunit=‘d’, /END <br/> ! &amp;GRIBOUT ! out02 <br/> ! yform_write=‘ncdf’, <br/> ! ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( <span class="caps"> NOUTDIR </span> +=1))]}, <br/> ! yvarml=‘W’,‘P’, <br/> ! yvarpl=’ ‘, <br/> ! yvarzl=’ ‘, <br/> ! luvmasspoint=.TRUE., <br/> ! lcheck = .FALSE., <br/> ! lwrite_const= ${LWRITE_CONST}, <br/> ! ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, <br/> ! ytunit=‘d’, <br/> ! /END <br/> ! &amp;GRIBOUT ! out03 <br/> ! yform_write=‘ncdf’, <br/> ! ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( <span class="caps"> NOUTDIR </span> +=1))]}, <br/> ! yvarml=‘ <span class="caps"> RAIN </span> _CON’,‘ <span class="caps"> SNOW </span> _CON’,‘ <span class="caps"> RAIN </span> _GSP’,‘ <span class="caps"> SNOW </span> _GSP’,‘ <span class="caps"> TOT </span> _PREC’, <br/> ! yvarpl=’ ‘, <br/> ! yvarzl=’ ‘, <br/> ! luvmasspoint=.TRUE., <br/> ! lcheck = .FALSE., <br/> ! lwrite_const= ${LWRITE_CONST}, ! ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, <br/> ! ytunit=‘d’, ! /END </p> <p> and then I got the following error: </p> <p> 137: <strong> —————————————————————————————— </strong> <br/> 137: * <span class="caps"> PROGRAM </span> <span class="caps"> TERMINATED </span> <span class="caps"> BECAUSE </span> OF <span class="caps"> ERRORS </span> DETECTED <br/> 137: * IN <span class="caps"> ROUTINE </span> : organize_data: input <br/> 138: <strong> —————————————————————————————— </strong> </p> <p> Cheers <br/> Mingyue </p>
MZ replied

user#270 wrote:
> Hello Mingyue,
>
> I mean the namelist of COSMO-CLM
>
> !!out01: > &GRIBOUT > yform_write='ncdf', > ncomb=${NSTART},${NNEXT},${NOUT_INC[$((NOUTDIR+=1))]}, > yvarml='FRESHSNW','QV_S','T_S','T_SNOW','T_SO','W_I','W_SNOW','W_SO', > 'PP','QC','QI','QR','QS','Z0','QV','T','U','V','W', !QG is only available in high-resolution runs > yvarpl=' ', > yvarzl=' ', > luvmasspoint=.FALSE., > lcheck = .FALSE., > lwrite_const= ${LWRITE_CONST}, > ydir='${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/', > ytunit='d', > /END >
>
> Throw away all variables in yvarml and leave only one.
>
> Bye,
> Ronny

Hi, Ronny,

I commented out all the output but ‘ FRESHSNW ’ in output01, (all the variables from the other output channel are also commented out), like this &GRIBOUT ! out01 yform_write=‘ncdf’, ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( NOUTDIR +=1))]},
! uncomment the next but one line if you plan double nesting yvarml=‘ FRESHSNW ’, !‘QV_S’,‘T_S’,‘T_SNOW’,‘T_SO’,‘W_I’,‘W_SNOW’,‘W_SO’, !‘PP’,‘QC’,‘QI’,‘QR’,‘QS’,‘QV’,‘T’,‘U’,‘V’, yvarpl=’ ‘, yvarzl=’ ‘, luvmasspoint=.FALSE., lcheck = .FALSE., lwrite_const= ${LWRITE_CONST}, ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’, ytunit=‘d’, /END
! &GRIBOUT ! out02
! yform_write=‘ncdf’,
! ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( NOUTDIR +=1))]},
! yvarml=‘W’,‘P’,
! yvarpl=’ ‘,
! yvarzl=’ ‘,
! luvmasspoint=.TRUE.,
! lcheck = .FALSE.,
! lwrite_const= ${LWRITE_CONST},
! ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’,
! ytunit=‘d’,
! /END
! &GRIBOUT ! out03
! yform_write=‘ncdf’,
! ncomb=${NSTART},${NNEXT},${NOUT_INC[$(( NOUTDIR +=1))]},
! yvarml=‘ RAIN _CON’,‘ SNOW _CON’,‘ RAIN _GSP’,‘ SNOW _GSP’,‘ TOT _PREC’,
! yvarpl=’ ‘,
! yvarzl=’ ‘,
! luvmasspoint=.TRUE.,
! lcheck = .FALSE.,
! lwrite_const= ${LWRITE_CONST}, ! ydir=’${OUTDIR}/${YYYY_MM}/out$(printf %02d $NOUTDIR)/’,
! ytunit=‘d’, ! /END

and then I got the following error:

137: ——————————————————————————————
137: * PROGRAM TERMINATED BECAUSE OF ERRORS DETECTED
137: * IN ROUTINE : organize_data: input
138: ——————————————————————————————

Cheers
Mingyue

View in channel
<p> You are using the subchain. Thus, please adapt the job_settings and check for </p> <p> <code> NESTING_STREAM=( 1 ) # If you want to use an output stream to save quantities as input for further downscaling put the number of the output streams here. HOUT_INC=(03:00:00 01:00:00 06:00:00 01:00:00 01:00:00 03:00:00 06:00:00 24:00:00 24:00:00 01:00:00 01:00:00 06:00:00 06:00:00) # time increment for each GRIBOUT hh:mm:ss </code> </p> <p> Modify it to <code> HOUT_INC=(03:00:00) </code> . Please also sent the file <span class="caps"> INPUT </span> _IO generated in the directory /joboutputs/cclm/19XX_01/. </p> <p> Bye Ronny </p>

  @ronnypetrik in #db0c232

<p> You are using the subchain. Thus, please adapt the job_settings and check for </p> <p> <code> NESTING_STREAM=( 1 ) # If you want to use an output stream to save quantities as input for further downscaling put the number of the output streams here. HOUT_INC=(03:00:00 01:00:00 06:00:00 01:00:00 01:00:00 03:00:00 06:00:00 24:00:00 24:00:00 01:00:00 01:00:00 06:00:00 06:00:00) # time increment for each GRIBOUT hh:mm:ss </code> </p> <p> Modify it to <code> HOUT_INC=(03:00:00) </code> . Please also sent the file <span class="caps"> INPUT </span> _IO generated in the directory /joboutputs/cclm/19XX_01/. </p> <p> Bye Ronny </p>
RP replied

You are using the subchain. Thus, please adapt the job_settings and check for

NESTING_STREAM=( 1 ) # If you want to use an output stream to save quantities as input for further downscaling put the number of the output streams here. HOUT_INC=(03:00:00 01:00:00 06:00:00 01:00:00 01:00:00 03:00:00 06:00:00 24:00:00 24:00:00 01:00:00 01:00:00 06:00:00 06:00:00) # time increment for each GRIBOUT hh:mm:ss

Modify it to HOUT_INC=(03:00:00) . Please also sent the file INPUT _IO generated in the directory /joboutputs/cclm/19XX_01/.

Bye Ronny

View in channel
<p> Dear Ronny </p> <p> I did as you mentioned, I am using <span class="caps"> COSMO </span> - <span class="caps"> CLM </span> v5.0, thus there isn’t a variable called <span class="caps"> NESTING </span> _STREAM in the job_settings. Nevertheless, I tried to change <span class="caps"> HOUT </span> _INC=(7 03:00:00 24:00:00 01:00:00 03:00:00 06:00:00 06:00:00 24:00:00) into <span class="caps"> HOUT </span> _INC=(1 03:00:00) I think here the 7 means <span class="caps"> NESTING </span> _STREAM=( 1 ). </p> <p> It stopped because of the same reason: Error writing netcdf 2D variable, can we now make sure that it is because of the netcdf libraries you mentioned before, could you please let me how should I proceeding in this point, where should I involve this “nc-config —all”. </p> <p> Thank you very much in advance! </p> <p> Regards <br/> Mingyue </p>

  @mingyuezhang in #f39d8d7

<p> Dear Ronny </p> <p> I did as you mentioned, I am using <span class="caps"> COSMO </span> - <span class="caps"> CLM </span> v5.0, thus there isn’t a variable called <span class="caps"> NESTING </span> _STREAM in the job_settings. Nevertheless, I tried to change <span class="caps"> HOUT </span> _INC=(7 03:00:00 24:00:00 01:00:00 03:00:00 06:00:00 06:00:00 24:00:00) into <span class="caps"> HOUT </span> _INC=(1 03:00:00) I think here the 7 means <span class="caps"> NESTING </span> _STREAM=( 1 ). </p> <p> It stopped because of the same reason: Error writing netcdf 2D variable, can we now make sure that it is because of the netcdf libraries you mentioned before, could you please let me how should I proceeding in this point, where should I involve this “nc-config —all”. </p> <p> Thank you very much in advance! </p> <p> Regards <br/> Mingyue </p>
MZ replied

Dear Ronny

I did as you mentioned, I am using COSMO - CLM v5.0, thus there isn’t a variable called NESTING _STREAM in the job_settings. Nevertheless, I tried to change HOUT _INC=(7 03:00:00 24:00:00 01:00:00 03:00:00 06:00:00 06:00:00 24:00:00) into HOUT _INC=(1 03:00:00) I think here the 7 means NESTING _STREAM=( 1 ).

It stopped because of the same reason: Error writing netcdf 2D variable, can we now make sure that it is because of the netcdf libraries you mentioned before, could you please let me how should I proceeding in this point, where should I involve this “nc-config —all”.

Thank you very much in advance!

Regards
Mingyue

View in channel
<p> If you compile the COSMOv5 on <span class="caps"> MISTRAL </span> , you have used a specific Fopts-File. If you are familiar with this files, then i would highly recommend to copy this files from COSMO6 Starter package and compile COSMOv5 using them. If you are not familiar with the details of this files, I would highly recommend to download COSMO6 starter package and to prevent from further investigation with COSMOv5. </p>

  @ronnypetrik in #801ebe8

<p> If you compile the COSMOv5 on <span class="caps"> MISTRAL </span> , you have used a specific Fopts-File. If you are familiar with this files, then i would highly recommend to copy this files from COSMO6 Starter package and compile COSMOv5 using them. If you are not familiar with the details of this files, I would highly recommend to download COSMO6 starter package and to prevent from further investigation with COSMOv5. </p>
RP replied

If you compile the COSMOv5 on MISTRAL , you have used a specific Fopts-File. If you are familiar with this files, then i would highly recommend to copy this files from COSMO6 Starter package and compile COSMOv5 using them. If you are not familiar with the details of this files, I would highly recommend to download COSMO6 starter package and to prevent from further investigation with COSMOv5.

View in channel
<p> Dear Community, </p> <p> I am working together with Mingyue to solve the problem she mentioned before. We successfully compiled the COSMOv5 and also made it run on Levante. Everything seems to work except for the writing of NetCDF restart files. The creation of NetCDF-output and every other step works without any problems. The <span class="caps"> CCLM </span> -job runs until almost the end and crashes when writing the restart file. In a test, it worked when writing the restart file as binary but this is not really an option for us. Also using COSMOv6 is only a last solution because we want to continue our 2500 years of simulation (almost 1000 years already done) with as few changes as possible. 0: <span class="caps"> OPEN </span> : ncdf-file: 0: /work/bb1201/b381165_bb1152//mythos500bc_CCLM/restarts/lrfd7476030100o.nc 0: <strong> —————————————————————————————— </strong> 0: * <span class="caps"> PROGRAM </span> <span class="caps"> TERMINATED </span> <span class="caps"> BECAUSE </span> OF <span class="caps"> ERRORS </span> DETECTED 0: * IN <span class="caps"> ROUTINE </span> : output_data 0: * 0: * <span class="caps"> ERROR </span> <span class="caps"> CODE </span> is 2035 0: * Error writing netcdf 2D variable 0: <strong> —————————————————————————————— </strong> 0: ————————————————————————————————————— 0: <span class="caps"> MPI </span> _ABORT was invoked on rank 0 in communicator <span class="caps"> MPI </span> _COMM_WORLD 0: with errorcode 2035. 0: 0: <span class="caps"> NOTE </span> : invoking <span class="caps"> MPI </span> _ABORT causes Open <span class="caps"> MPI </span> to kill all <span class="caps"> MPI </span> processes. 0: You may or may not see output from other processes, depending on 0: exactly when Open <span class="caps"> MPI </span> kills them. 0: ————————————————————————————————————— <br/> srun: Job step aborted: Waiting up to 302 seconds for job step to finish. 0: slurmstepd: error: *** <span class="caps"> STEP </span> 1344625.0 ON l30116 <span class="caps"> CANCELLED </span> AT 2022-08-03T09:49:15 *** <br/> srun: error: l30116: task 0: Exited with exit code 243 <br/> srun: launch/slurm: _step_signal: Terminating StepId=1344625.0 <br/> srun: error: l30116: tasks 1-143: Killed <br/> srun: error: l30117: tasks 144-287: Killed </p> <p> Does anyone know about the differences between writing the output and writing the restart file? Or did anyone have to deal with similar problems? <br/> We would be very happy about any suggestion and help. </p> <p> Thank you very much and kind regards, <br/> Eva </p>

  @evanowatzki in #a83f01d

<p> Dear Community, </p> <p> I am working together with Mingyue to solve the problem she mentioned before. We successfully compiled the COSMOv5 and also made it run on Levante. Everything seems to work except for the writing of NetCDF restart files. The creation of NetCDF-output and every other step works without any problems. The <span class="caps"> CCLM </span> -job runs until almost the end and crashes when writing the restart file. In a test, it worked when writing the restart file as binary but this is not really an option for us. Also using COSMOv6 is only a last solution because we want to continue our 2500 years of simulation (almost 1000 years already done) with as few changes as possible. 0: <span class="caps"> OPEN </span> : ncdf-file: 0: /work/bb1201/b381165_bb1152//mythos500bc_CCLM/restarts/lrfd7476030100o.nc 0: <strong> —————————————————————————————— </strong> 0: * <span class="caps"> PROGRAM </span> <span class="caps"> TERMINATED </span> <span class="caps"> BECAUSE </span> OF <span class="caps"> ERRORS </span> DETECTED 0: * IN <span class="caps"> ROUTINE </span> : output_data 0: * 0: * <span class="caps"> ERROR </span> <span class="caps"> CODE </span> is 2035 0: * Error writing netcdf 2D variable 0: <strong> —————————————————————————————— </strong> 0: ————————————————————————————————————— 0: <span class="caps"> MPI </span> _ABORT was invoked on rank 0 in communicator <span class="caps"> MPI </span> _COMM_WORLD 0: with errorcode 2035. 0: 0: <span class="caps"> NOTE </span> : invoking <span class="caps"> MPI </span> _ABORT causes Open <span class="caps"> MPI </span> to kill all <span class="caps"> MPI </span> processes. 0: You may or may not see output from other processes, depending on 0: exactly when Open <span class="caps"> MPI </span> kills them. 0: ————————————————————————————————————— <br/> srun: Job step aborted: Waiting up to 302 seconds for job step to finish. 0: slurmstepd: error: *** <span class="caps"> STEP </span> 1344625.0 ON l30116 <span class="caps"> CANCELLED </span> AT 2022-08-03T09:49:15 *** <br/> srun: error: l30116: task 0: Exited with exit code 243 <br/> srun: launch/slurm: _step_signal: Terminating StepId=1344625.0 <br/> srun: error: l30116: tasks 1-143: Killed <br/> srun: error: l30117: tasks 144-287: Killed </p> <p> Does anyone know about the differences between writing the output and writing the restart file? Or did anyone have to deal with similar problems? <br/> We would be very happy about any suggestion and help. </p> <p> Thank you very much and kind regards, <br/> Eva </p>
EH replied

Dear Community,

I am working together with Mingyue to solve the problem she mentioned before. We successfully compiled the COSMOv5 and also made it run on Levante. Everything seems to work except for the writing of NetCDF restart files. The creation of NetCDF-output and every other step works without any problems. The CCLM -job runs until almost the end and crashes when writing the restart file. In a test, it worked when writing the restart file as binary but this is not really an option for us. Also using COSMOv6 is only a last solution because we want to continue our 2500 years of simulation (almost 1000 years already done) with as few changes as possible. 0: OPEN : ncdf-file: 0: /work/bb1201/b381165_bb1152//mythos500bc_CCLM/restarts/lrfd7476030100o.nc 0: —————————————————————————————— 0: * PROGRAM TERMINATED BECAUSE OF ERRORS DETECTED 0: * IN ROUTINE : output_data 0: * 0: * ERROR CODE is 2035 0: * Error writing netcdf 2D variable 0: —————————————————————————————— 0: ————————————————————————————————————— 0: MPI _ABORT was invoked on rank 0 in communicator MPI _COMM_WORLD 0: with errorcode 2035. 0: 0: NOTE : invoking MPI _ABORT causes Open MPI to kill all MPI processes. 0: You may or may not see output from other processes, depending on 0: exactly when Open MPI kills them. 0: —————————————————————————————————————
srun: Job step aborted: Waiting up to 302 seconds for job step to finish. 0: slurmstepd: error: *** STEP 1344625.0 ON l30116 CANCELLED AT 2022-08-03T09:49:15 ***
srun: error: l30116: task 0: Exited with exit code 243
srun: launch/slurm: _step_signal: Terminating StepId=1344625.0
srun: error: l30116: tasks 1-143: Killed
srun: error: l30117: tasks 144-287: Killed

Does anyone know about the differences between writing the output and writing the restart file? Or did anyone have to deal with similar problems?
We would be very happy about any suggestion and help.

Thank you very much and kind regards,
Eva

View in channel
<p> HEllo, </p> <p> you did everything right with your Fopts file. Nice to hear, that now the output of netcdf-files works properly. However, restart-netcdf is not written. Regarding this I would recommend two things: <br/> 1) Keep sure that you use the most recent version of COSMOv5 provided by Burhkardt Rockel on our <span class="caps"> REDC </span> homepages (as the netcdf-restart functionality is very new and made some problems). <br/> 2) Be happy with what you achieved so far and change to binary restarts. It will not affect your integration. </p> <p> Bye, <br/> Ronny </p>

  @ronnypetrik in #1ac8bf9

<p> HEllo, </p> <p> you did everything right with your Fopts file. Nice to hear, that now the output of netcdf-files works properly. However, restart-netcdf is not written. Regarding this I would recommend two things: <br/> 1) Keep sure that you use the most recent version of COSMOv5 provided by Burhkardt Rockel on our <span class="caps"> REDC </span> homepages (as the netcdf-restart functionality is very new and made some problems). <br/> 2) Be happy with what you achieved so far and change to binary restarts. It will not affect your integration. </p> <p> Bye, <br/> Ronny </p>
RP replied

HEllo,

you did everything right with your Fopts file. Nice to hear, that now the output of netcdf-files works properly. However, restart-netcdf is not written. Regarding this I would recommend two things:
1) Keep sure that you use the most recent version of COSMOv5 provided by Burhkardt Rockel on our REDC homepages (as the netcdf-restart functionality is very new and made some problems).
2) Be happy with what you achieved so far and change to binary restarts. It will not affect your integration.

Bye,
Ronny

View in channel