pio error when building cesm1_2_2_CAMChem

[li230@illinois_edu]

Hi, I just downloaded the source code from https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2_CAMChem/, and build a case by calling ./create_newcase -case /glade/scratch/yinruili/cases/$CASE-res f19_f19 -mach yellowstone -compset FSTRATMAM4, and called ./cesm_setup in the case directory. However when I try ./casename.build, I got an error:ERROR: buildlib.pio failed, see /glade/scratch/yinruili/cesm1_2_2_CAMChem.MAM4_test10/bld/intel/mpich2/nodebug/threads/pio.bldlog.160518-121539 ERROR: cat /glade/scratch/yinruili/cesm1_2_2_CAMChem.MAM4_test10/bld/intel/mpich2/nodebug/threads/pio.bldlog.160518-121539It seems that there is no pio file in my source code. I also checked http://parallelio.googlecode.com/svn/trunk_tags/pio1_8_12/pio but got a 404 error.I attached my pio log here. Actually I have downloaded cesm1_2_2_CAMChem from https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2_CAMChem/ a few month ago and have successfully run the case on Yellowstone. I deleted the source code by mistake so I downloaded it again, but this time I couldn't find the pio file in /models/utils. I use svn co https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2_CAMChem/ cesm1_2_2_CAMChem to download the code....Is that fine? Thanks!Yinrui

 

[jedwards]

googlecode repositories are now off line, we are very sorry for the inconvenience.    Here are the changes that you needsubstitute the version numbers in your version for the ones below:In the tools/cprnc/SVN_EXTERNAL_FILES change:-genf90 http://parallelio.googlecode.com/svn/genf90/trunk_tags/genf90_140121+genf90 https://github.com/PARALLELIO/genf90/tags/genf90_140121 In the top level SVN_EXTERNAL_DIRECTORIES change:-models/utils/pio                   http://parallelio.googlecode.com/svn/trunk_tags/pio1_8_12/pio+models/utils/pio                   https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio 

 

[ihmn_zgz@gmail_com]

Hello,I also have this same problem that there is no pio directory. I followed your instructions, but in the tools/cprnc/ directory:1) There is no such file as SVN_EXTERNAL_FILES in the tools/cprnc/ directory.2) The content of SVN_EXTERNAL_DIRECTORIES is genf90 http://parallelio.googlecode.com/svn/genf90/trunk_tags/genf90_1401213) The page https://github.com/PARALLELIO/genf90/tags/genf90_140121 does not exist. There is however https://github.com/PARALLELIO/genf90/releases/tag/genf90_140121 . I guess this is the correct one?4) The page https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio does not exist. I don't find any other one that could be the correct one. So I'm supposed to write non-existing adresses in files that don't exist or cointain something different that there are supposed to? I'm very confused, please help. Can't I download the pio directory to where it should be, wouldn't that work?
Thanks in advance

 

[jedwards]

You are correct those pages do not exist - github does some magic though so that if you trysvn checkout https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio you will get the code you seek. 

 

[ihmn_zgz@gmail_com]

Magic happened! However there is no "Makefile" file inside the pio I just downloaded, and keeps giving me error because it looks for this file.I've seen that there is a https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pilgrim inside where there is a "Makefile" file. Currenly I'm working in cesm1.2.1, but I previously downloaded by mistake a ccsm4 copy that includes the pio/ directory and also a pilgrim/ directory that I don't have in my cesm1.2.1 copy. Inside the ccsm4 pilgrim/ directory there is no "Makefile" but there is one inside pio/. I also compared these two "Makefile" files and there are slightly different, so I'm not sure which should I use.  So... should I 1) Copy the pio and pilgrim directories from the ccsm4 into the cesm1.2.1 copy, or 2) download the https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pilgrim and move the Makefile it contains into the pio/ directory, or 3) neither of those?Thanks in advance, sorry if I'm being anoying.

 

[jedwards]

pio and pilgrim have nothing to do with each other.You probably failed to completely clean the bld directory before you tried to build again.  Try again after rm -fr $CASE/bld or with a completly new case. 

 

[ihmn_zgz@gmail_com]

Ok, I removed the bld and run the test again, didn't worked. Then I tried with a completely new case. I obtained the same error.ERROR: buildlib.pio failed, see /home/hermoso0/scratch/hugoteam/test2/bld/pio/pio.bldlog.160819-160224
ERROR: cat /home/hermoso0/scratch/hugoteam/test2/bld/pio/pio.bldlog.160819-160224Here is the content of pio.bldlog.160819-160224: Fri Aug 19 16:05:55 ADT 2016 /home/hermoso0/scratch/hugoteam/test2/bld/pio/pio.bldlog.160819-160224
Copying source to CCSM EXEROOT...
cp: cannot stat `/home/hermoso0/scratch/cesm1_2_1/models/utils/pio/Makefile': No such file or directory
New build of PIO
Running configure...
for OS=LINUX MACH=userdefined
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
/home/hermoso0/scratch/cesm1_2_1/scripts/test2/Tools/mkSrcfiles
cp -f /home/hermoso0/scratch/hugoteam/test2/bld/pio/Filepath /home/hermoso0/scratch/hugoteam/test2/bld/pio/Deppath
/home/hermoso0/scratch/cesm1_2_1/scripts/test2/Tools/mkDepends  Deppath Srcfiles > /home/hermoso0/scratch/hugoteam/test2/bld/pio/Depends
cd /home/hermoso0/scratch/hugoteam/test2/bld/pio;
     /home/hermoso0/scratch/cesm1_2_1/models/utils/pio/configure  --enable-timing CC="icc " FC="ifort " MPICC="mpicc  " MPIFC="mpif90 " FCFLAGS="-O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback  -free  -I.  -I/home/hermoso0/scratch/hugoteam/test2/bld/pio -I/usr/local/netcdf.intel-4.2/include -I/usr/local/openmpi.intel-1.8.8/include -I/home/hermoso0/scratch/hugoteam/test2/bld/mct/mct -I/home/hermoso0/scratch/hugoteam/test2/bld/mct/mpeu -I/home/hermoso0/scratch/hugoteam/test2/bld/pio -I/home/hermoso0/scratch/hugoteam/test2/bld/gptl -I/home/hermoso0/scratch/cesm1_2_1/models/utils/pio -I/home/hermoso0/scratch/hugoteam/test2/bld/lib/include" CPPDEFS=" -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC" CFLAGS="-O2 -fp-model precise   -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC -I.. -I.  -I/home/hermoso0/scratch/hugoteam/test2/bld/pio -I/usr/local/netcdf.intel-4.2/include -I/usr/local/openmpi.intel-1.8.8/include -I/home/hermoso0/scratch/hugoteam/test2/bld/mct/mct -I/home/hermoso0/scratch/hugoteam/test2/bld/mct/mpeu -I/home/hermoso0/scratch/hugoteam/test2/bld/pio -I/home/hermoso0/scratch/hugoteam/test2/bld/gptl -I/home/hermoso0/scratch/cesm1_2_1/models/utils/pio -I/home/hermoso0/scratch/hugoteam/test2/bld/lib/include" NETCDF_PATH=/usr/local/netcdf.intel-4.2 LDFLAGS="" LIBS=""   --srcdir /home/hermoso0/scratch/cesm1_2_1/models/utils/pio
/bin/sh: line 1: /home/hermoso0/scratch/cesm1_2_1/models/utils/pio/configure: No such file or directory
gmake: *** [/home/hermoso0/scratch/hugoteam/test2/bld/pio/Makefile.conf] Error 127
cp: cannot stat `Makefile.conf': No such file or directory
gmake: *** No targets specified and no makefile found.  Stop. Indeed, there is no 'Makefile' or 'configure' files inside the /pio directory I downloaded into /home/hermoso0/scratch/cesm1_2_1/models/utils/ with your link.

 

[ihmn_zgz@gmail_com]

I decided to download and use CESM1.2.0, which does include the pio directory, instead of 1.2.1. That solved this problem.

 

[ihmn_zgz@gmail_com]

Okey, I've solved the problem. I post it in case somebody else has the problem so they don't get stuck as I did.The problem is that I was downloading both pio and genf90 into models/utils. When I downloaded cesm1.2.0 that has both directories downloaded into the correct places, I saw that genf90 should be in tools/cprnc. Once I corrected that, I didn't get error any more. Thanks for the help