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geoschem / geos-chem

GEOS-Chem "Science Codebase" repository. Contains GEOS-Chem science routines, run directory generation scripts, and interface code. This repository is used as a submodule within the GCClassic and GCHP wrappers, as well as in other modeling contexts (external ESMs).
http://geos-chem.org
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geos-chem 13.1.2 netcdf I/O (new user) #792

Closed clearsky112 closed 3 years ago

clearsky112 commented 3 years ago

### Description of the problem

I am a new user.

  1. I downloaded the code from https://github.com/geoschem/GCClassic git clone https://github.com/geoschem/GCClassic.git GCClassic.13
  2. In the GCClassic.13 folder went to ./run and used createRunDir.sh to create a run directory
  3. In the run directory run cmake commands and first had issue:

[100%] Linking Fortran executable ../bin/gcclassic /data/mmb/raqm/work/repos/code/2018_SIP/libraries_intel19.1.3.304/nc4hdf5/lib/libnetcdf.a(libnchdf5_la-hdf5file.o): In function nc4_enddef_netcdf4_file': hdf5file.c:(.text+0x54c): undefined reference toH5Fflush'

I used the netcdf4+hdf5. I thought it might be hdf5 issue, so I switched netcdf to the netcdf libraries (without HDF5), then cmake worked and I could generate ./gcclassic

  1. Then I did the dry-run test, using download_data.py and ./gcclassic --dryrun, everything looked ok.

  2. tested a case (not dry run). So I just run ./gcclassic, then I got issues:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

In Ncop_Rd, cannot open: /home/ycui/ExtData/HEMCO/XIAO/v2014-09/C3H8_C2H6_ngas.geos.1x1.nc

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Code stopped from DO_ERR_OUT (in module NcdfUtil/m_do_err_out.F90)

This is an error that was encountered in one of the netCDF I/O modules, which indicates an error in writing to or reading from a netCDF file!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

### Description of troubleshooting performed no

### GEOS-Chem version GEOS-Chem 13.1.2

### Description of modifications no

### Log files

### Software versions

yangzhenlin-hub commented 1 year ago

Hello, how do you solve this problem?

clearsky112 commented 1 year ago

I re-downloaded the file and then it worked.

yangzhenlin-hub commented 1 year ago

好哒，谢谢您！！！

------------------ 原始邮件 ------------------ 发件人: "geoschem/geos-chem" @.>; 发送时间: 2022年11月15日(星期二) 中午1:26 @.>; 抄送: "◇﹎兔.子~` @.**@.>; 主题: Re: [geoschem/geos-chem] geos-chem 13.1.2 netcdf I/O (new user) (#792)

I re-downloaded the file and then it worked.

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