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ERROR in ./case.build

J

jialiu

NJNU
Member
Hi all,
I have run into an error when run ./case.build
Check the cesmlog file, I have find the following error.
L/share/home/lilonghui/lilonghui_wangqing/cesm2/liu/FCHIST/bld/intel/impi/nodebug/nothreads/mct/lib -lpio -lgptl -lmct -lmpeu -L/share/home/lilonghui/apps/intel2020/netcdf-4.7.4-parallel//lib -lnetcdff -lnetcdf -mkl=cluster -L/share/apps/intel/oneapi/basekit/2021.4.0.3422/mpi/2021.4.0//lib -lmpi
ifort: command line remark #10412: option '-mkl=cluster' is deprecated and will be removed in a future release. Please use the replacement option '-qmkl=cluster'
ld: cannot find -lmkl_intel_lp64
ld: cannot find -lmkl_cdft_core
ld: cannot find -lmkl_scalapack_lp64
ld: cannot find -lmkl_blacs_intelmpi_lp64
ld: cannot find -lmkl_sequential
ld: cannot find -lmkl_core
make: *** [/share/home/*/cesm2/liu/FCHIST/bld/cesm.exe] Error 1
Any help is highly appreciated.
 

Attachments

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  • cesm.bldlog.txt
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J

jedwards

CSEG and Liaisons
Staff member
Intel has changed the -mkl=cluster flag to be -qmkl=cluster I think that the mkl library should be provided
in the intel 2021 version that you are using. Check with your system staff.
 
L

liviasancho@gmail_com

New Member
Hello, I am also having a building problem. I created a new case on a rocky linux 8.5 machine. I'm using Modules Release 4.5.2 (2020-07-30) and CESM2.1.3.

I am successful in creating the case and perform case.setup
./create_newcase --machine centos7-linux --case /disco2/cesm/cases/b.day1.0 --res f19_g17 --compset B1850
./case.setup

But when I try to build it, some error occur downloading the data:

(base) [numa19@ire0233 b.day1.0]$ ./case.build
Building case in directory /disco2/cesm/cases/b.day1.0
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Refcase not found in /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01, will attempt to download from inputdata
Checking server ftp://gridanon.cgd.ucar.edu:2811/cesm/inputdata/ with protocol gftp
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Client protocol gftp not enabled
Checking server ftp://ftp.cgd.ucar.edu/cesm/inputdata with protocol wget
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol wget with user anonymous and passwd user@example.edu
Could not connect to repo 'ftp://ftp.cgd.ucar.edu/cesm/inputdata'
This is most likely either a proxy, or network issue .
Checking server ftp.cgd.ucar.edu/cesm/inputdata with protocol ftp
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol ftp with user anonymous and passwd user@example.edu
server address ftp.cgd.ucar.edu root path cesm/inputdata
ftp login timeout! [Errno 110] Connection timed out
Checking server https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata with protocol svn
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol svn with user and passwd
Loading input file list: 'Buildconf/refcase.input_data_list'
Model refcase missing file refdir = '/disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/'
Trying to download file: 'cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01' to path '/disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01' using SVN protocol.
Creating directory /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01
SUCCESS

ERROR: Failed to find or download file /disco2/cesm/archive/b.day1.0/run/inputdata_checksum.dat

If I try to re-build it:

(base) [numa19@ire0233 b.day1.0]$ ./case.build
Building case in directory /disco2/cesm/cases/b.day1.0
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
- Prestaging REFCASE (/disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01) to /disco2/cesm/archive/b.day1.0/run
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ocn.restart
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.rof
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ocn.ovf
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.drv
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.lnd
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.glc
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ice
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.atm
Copy rpointer /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ocn.tavg.5
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.cam.i.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.mosart.r.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.cpl.r.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.cice.r.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.cam.r.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.pop.ro.0301-01-01-00000
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.ww3.r.0301-01-01-00000
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.clm2.r.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.cam.rs.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.cism.r.0301-01-01-00000.nc
Staging file /disco2/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/b.e20.B1850.f19_g17.release_cesm2_1_0.020.pop.r.0301-01-01-00000.nc
Creating component namelists
Calling /home/numa19/cesm/cesm2.1.3/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /disco2/cesm/cases/b.day1.0/Buildconf/camconf/atm_in file2 /disco2/cesm/archive/b.day1.0/run/atm_in
Calling /home/numa19/cesm/cesm2.1.3/components/clm//cime_config/buildnml
Calling /home/numa19/cesm/cesm2.1.3/components/cice//cime_config/buildnml
...buildnml calling cice buildcpp to set build time options
File not found: grid_file = "/disco2/cesm/inputdata/ocn/pop/gx1v7/grid/horiz_grid_20010402.ieeer8", will attempt to download in check_input_data phase
File not found: kmt_file = "/disco2/cesm/inputdata/ocn/pop/gx1v7/grid/topography_20161215.ieeei4", will attempt to download in check_input_data phase
Calling /home/numa19/cesm/cesm2.1.3/components/pop//cime_config/buildnml
... buildnml: calling pop buildcpp to set build time options
ERROR: Command /home/numa19/cesm/cesm2.1.3/components/pop/bld/build-namelist failed rc=2
out=
err=env: ‘/home/numa19/cesm/cesm2.1.3/components/pop/input_templates/ocn.base.tavg.csh’: No such file or directory
ERROR ocn.base.tavg.csh: env CASEBUILD=/disco2/cesm/cases/b.day1.0/Buildconf OCN_GRID=gx1v7 /home/numa19/cesm/cesm2.1.3/components/pop/input_templates/ocn.base.tavg.csh failed: 32512

What am I missing here?

Any help will be much appreciated!
 
J

jedwards

CSEG and Liaisons
Staff member
Looks like you are missing file /home/numa19/cesm/cesm2.1.3/components/pop/input_templates/ocn.base.tavg.csh
try cd components/pop
git checkout -- input_templates/ocn.base.tavg.csh
 
J

jialiu

NJNU
Member
jedwards said:
Intel has changed the -mkl=cluster flag to be -qmkl=cluster I think that the mkl library should be provided
in the intel 2021 version that you are using. Check with your system staff.
Click to expand...
Thanks for you reminding. It is really useful！1652841034576.png
 
L

liviasancho@gmail_com

New Member
jedwards said:
Looks like you are missing file /home/numa19/cesm/cesm2.1.3/components/pop/input_templates/ocn.base.tavg.csh
try cd components/pop
git checkout -- input_templates/ocn.base.tavg.csh
Click to expand...
Hi Jim! Sorry for the delayed response:

I actually have this file, but CESM doesn't seem to find it.

(base) [numa19@ire0233 input_templates]$ pwd
/home/numa19/cesm/cesm2.1.3/components/pop/input_templates
(base) [numa19@ire0233 input_templates]$ ls ocn.base.tavg.csh
ocn.base.tavg.csh
 
J

jedwards

CSEG and Liaisons
Staff member
The error code 32512 is a perl return value from script pop/bld/build-namelist
indicating that the file was not found. But the file is there, I've puzzled over this and don't understand why
you would get this error.
 
M

mlevy

Michael Levy
CSEG and Liaisons
Staff member
Could you do the following, please?

Code: 
$ cd /home/numa19/cesm/cesm2.1.3/components/pop/input_templates
$ git status
$ ls -l ocn.base.tavg.csh

I wonder if either (a) the permissions on the file got messed up, or (b) the file is somehow corrupt.
 
L

liviasancho@gmail_com

New Member
Hello! Here are the returns from the commands:

(base) [numa19@ire0233 input_templates]$ pwd
/home/numa19/cesm/cesm2.1.3/components/pop/input_templates

(base) [numa19@ire0233 input_templates]$ git status
HEAD detached at pop2_cesm2_1_rel_n09
Untracked files:
(use "git add <file>..." to include in what will be committed)
../MARBL_scripts/MARBL_wrappers/__pycache__/
../cime_config/__pycache__/
../externals/CVMix/
../externals/MARBL/

nothing added to commit but untracked files present (use "git add" to track)

(base) [numa19@ire0233 input_templates]$ ls -l ocn.base.tavg.csh
-rwxrwxr-x. 1 numa19 numa19 1704 Apr 6 07:25 ocn.base.tavg.csh

(base) [numa19@ire0233 input_templates]$


mlevy said:
Could you do the following, please?

Code: 
$ cd /home/numa19/cesm/cesm2.1.3/components/pop/input_templates
$ git status
$ ls -l ocn.base.tavg.csh

I wonder if either (a) the permissions on the file got messed up, or (b) the file is somehow corrupt.
Click to expand...
 
T

taoliu_tech

Tao Liu
Member
liviasancho@gmail_com said:
Hello! Here are the returns from the commands:

(base) [numa19@ire0233 input_templates]$ pwd
/home/numa19/cesm/cesm2.1.3/components/pop/input_templates

(base) [numa19@ire0233 input_templates]$ git status
HEAD detached at pop2_cesm2_1_rel_n09
Untracked files:
(use "git add <file>..." to include in what will be committed)
../MARBL_scripts/MARBL_wrappers/__pycache__/
../cime_config/__pycache__/
../externals/CVMix/
../externals/MARBL/

nothing added to commit but untracked files present (use "git add" to track)

(base) [numa19@ire0233 input_templates]$ ls -l ocn.base.tavg.csh
-rwxrwxr-x. 1 numa19 numa19 1704 Apr 6 07:25 ocn.base.tavg.csh

(base) [numa19@ire0233 input_templates]$
Click to expand...
Did you solve the error? I got the same issue. I can find ocn.base.tavg.csh in that folder, but cesm is still complaining that it can not find ocn.base.tavg.csh
 
J

jedwards

CSEG and Liaisons
Staff member
Can you run the command from the command line?
Code: 
env CASEBUILD=/disco2/cesm/cases/b.day1.0/Buildconf OCN_GRID=gx1v7   /home/numa19/cesm/cesm2.1.3/components/pop/input_templates/ocn.base.tavg.csh

Replace the paths with appropriate ones for your system
 
T

taoliu_tech

Tao Liu
Member
jedwards said:
Can you run the command from the command line?
Code: 
env CASEBUILD=/disco2/cesm/cases/b.day1.0/Buildconf OCN_GRID=gx1v7   /home/numa19/cesm/cesm2.1.3/components/pop/input_templates/ocn.base.tavg.csh

Replace the paths with appropriate ones for your system
Click to expand...
I solved the error ocn.base.tavg.csh after I installed csh on my machine using "sudo apt-get install csh" following the instruction here Build error with 'ocn.base.tavg.csh' error · Issue #74 · ESCOMP/CESM.
However, now I got another error below
/home/taoliu/anaconda3/envs/gxx/bin/x86_64-conda-linux-gnu-ar: two different operation options specified
gmake[1]: *** [libmpeu.a] Error 1
 
J

jedwards

CSEG and Liaisons
Staff member
Check the values of AR and ARFLAGS in your environment or try
unset AR
unset ARFLAGS
./case.build
 
T

taoliu_tech

Tao Liu
Member
jedwards said:
Check the values of AR and ARFLAGS in your environment or try
unset AR
unset ARFLAGS
./case.build
Click to expand...
I solved the error "two different operation options specified" by exiting conda environment using "conda deactivate", because one thread said conda environment can cause this issue.
However, not after I ran ./case.build I got the error below.
collect2: error: ld returned 1 exit status

One thread relevant to the error above(Unable to build the case) suggested using netcdf-c 4.9.0. However, I indeed used netcdf-c 4.9.0. I am using ./create_newcase --case test4 --compset B1850 --res f19_g17 --mach mtu to create this test case. I ported machine to my Linux Ubuntu 18.04.6 server. Not sure what to do next.
 
J

jedwards

CSEG and Liaisons
Staff member
I don't know what collect2 is, I don't think that it's part of cesm. What is the context of the current error?
 
T

taoliu_tech

Tao Liu
Member
jedwards said:
I don't know what collect2 is, I don't think that it's part of cesm. What is the context of the current error?
Click to expand...
I just solved this error by adding the text below to the config_compilers.xml. Now, I can build the case successfully.
<SLIBS>
<append> -llapack -lblas </append>
</SLIBS>

However, after I finished running ./case.submit, I found all the hist folders under the archive are empty. The log file shows the message below. What does this mean?
[u112171:12711] [[58613,0],0] ORTE_ERROR_LOG: The system limit on number of pipes a process can open was reached in file odls_default_module.c at line 689
 
T

taoliu_tech

Tao Liu
Member
jedwards said:
I've not seen that message before but it looks like a recursive loop of some kind.
Click to expand...
That error disappeared after I decreased the <MAX_TASKS_PER_NODE>128</MAX_TASKS_PER_NODE> to <MAX_TASKS_PER_NODE>32</MAX_TASKS_PER_NODE> in the config_machines.xml.

However, the ./case.submit is not successful. Another error came up, as shown below.
[u112171:59692] *** An error occurred in MPI_Irecv
[u112171:59692] *** reported by process [1014038529,0]
[u112171:59692] *** on communicator MPI COMMUNICATOR 4 DUP FROM 3
[u112171:59692] *** MPI_ERR_COUNT: invalid count argument
[u112171:59692] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[u112171:59692] *** and potentially your MPI job)

This thread(MPI run error message.) seems to get the same error.
 

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