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GoogleCode Repositories are Offline PIO source not found

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jedwards
GoogleCode Repositories are Offline PIO source not found

Affected Releases CESM1.0.z
Affected Releases CESM1.1.z
Affected Releases CESM1.2.z

 

Googlecode repositories are now off line and the pio and genf90 components of older cesm versions can no longer resolve.  We are very sorry for the inconvenience.    Here are the changes that you need

substitute the version numbers in your version for the ones below:

In the tools/cprnc/SVN_EXTERNAL_DIRECTORIES 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

 

After each of the above changes run

$ svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES .

$ svn update

CESM Software Engineer

sang-ki.lee@...

Hi,

I think that "/tools/cprnc/SVN_EXTERNAL_FILES" should be "/tools/cprnc/SVN_EXTERNAL_DIRECTORIES".

And, I tried "svn propset svn:externals -F SVN_EXTERNAL_DIRECTORIES .", but did not work for me. So, I tried the following commands to download the necessary files:

svn export --force https://github.com/PARALLELIO/genf90/tags/genf90_140121 ./cesm1_2_2/tools/cprnc/genf90

svn export --force https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio ./cesm1_2_2/models/utils/pio

Do you think that this will do?

Thanks,

Sang-Ki

Dr. Sang-Ki Lee
NOAA/AOML
4301 Rickenbacker Causeway Miami,
FL 33149 USA
Tel) 305-361-4521
Fax) 305-361-4412
E-mail) eval(unescape('%64%6f%63%75%6d%65%6e%74%2e%77%72%69%74%65%28%27%3c%61%20%68%72%65%66%3d%22%6d%61%69%6c%74%6f%3a%73%61%6e%67%2d%6b%69%2e%6c%65%65%40%6e%6f%61%61%2e%67%6f%76%22%3e%73%61%6e%67%2d%6b%69%2e%6c%65%65%40%6e%6f%61%61%2e%67%6f%76%3c%2f%61%3e%27%29%3b'))

enver.ramirez@...

In terms of export the code your suggestion works for me.

gmodica@...

After updating for the missing PIO utils per your reply, my PIO build failed for lack of a PIO Makefile, which does appear to be included in the repository (nor is configure). What's the likely cause of my missing PIO Makefile and configure files?

$ cat /home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio/pio.bldlog.170126-164457
Thu Jan 26 16:45:24 UTC 2017 /home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio/pio.bldlog.170126-164457
Copying source to CCSM EXEROOT...
cp: cannot stat ‘/home/ec2-user/AWS-CESM/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/ec2-user/AWS-CESM/cesm1_2_1/test1/Tools/mkSrcfiles
cp -f /home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio/Filepath /home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio/Deppath
/home/ec2-user/AWS-CESM/cesm1_2_1/test1/Tools/mkDepends  Deppath Srcfiles > /home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio/Depends
cd /home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio; \
 /home/ec2-user/AWS-CESM/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/ec2-user/AWS-CESM/cesm1_2_1/test1/pio -I/data/RESOURCES/Intel/netcdf4.4/include -I/data/RESOURCES/Intel/lib/include -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/mct/mct -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/mct/mpeu -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/gptl -I/home/ec2-user/AWS-CESM/cesm1_2_1/models/utils/pio -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/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/ec2-user/AWS-CESM/cesm1_2_1/test1/pio -I/data/RESOURCES/Intel/netcdf4.4/include -I/data/RESOURCES/Intel/lib/include -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/mct/mct -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/mct/mpeu -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/gptl -I/home/ec2-user/AWS-CESM/cesm1_2_1/models/utils/pio -I/home/ec2-user/AWS-CESM/cesm1_2_1/test1/lib/include" NETCDF_PATH=/data/RESOURCES/Intel/netcdf4.4 LDFLAGS="" LIBS="-L/data/RESOURCES/Intel/lib -lnetcdff -L/data/RESOURCES/Intel/lib -lnetcdf -lnetcdf"   --srcdir /home/ec2-user/AWS-CESM/cesm1_2_1/models/utils/pio
/bin/sh: line 1: /home/ec2-user/AWS-CESM/cesm1_2_1/models/utils/pio/configure: No such file or directory
gmake: *** [/home/ec2-user/AWS-CESM/cesm1_2_1/test1/pio/Makefile.conf] Error 127
cp: cannot stat ‘Makefile.conf’: No such file or directory
gmake: *** No targets specified and no makefile found.  Stop.

AER_GM

jedwards

Makefile should be generated by configure, configure is missing - are you sure that you have a good checkout of the code?

ls -l /home/ec2-user/AWS-CESM/cesm1_2_1/models/utils/pio/configure

CESM Software Engineer

gmodica@...

I am not sure I have a good checkout. I tried 'svn update' in my utils/pio directory, but that didn't appear to replace my configure and Makefile.

$ ll /home/ec2-user/AWS-CESM/cesm1_2_1/models/utils/pio
total 1608
drwxrwxr-x 3 ec2-user ec2-user   4096 Jan 26 19:21 ./
drwxrwxr-x 6 ec2-user ec2-user   4096 Jan 24 21:15 ../
-rwxr--r-- 1 ec2-user ec2-user  27677 Jan 24 21:15 alloc_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user   7557 Jan 24 21:15 alloc_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user  82727 Jan 24 21:15 box_rearrange.F90*
-rwxr--r-- 1 ec2-user ec2-user  49657 Jan 24 21:15 box_rearrange.F90.in*
-rwxr--r-- 1 ec2-user ec2-user   8910 Jan 24 21:15 calcdecomp.F90*
-rwxr--r-- 1 ec2-user ec2-user   9340 Jan 24 21:15 calcdisplace_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user  16322 Jan 24 21:15 C_interface_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user   6953 Jan 24 21:15 CMakeLists.txt*
-rwxr--r-- 1 ec2-user ec2-user   2112 Jan 24 21:15 config.h.in*
-rwxr--r-- 1 ec2-user ec2-user    106 Jan 24 21:15 dtypes.h*
-rwxr--r-- 1 ec2-user ec2-user   1290 Jan 24 21:15 fdepends.awk*
-rwxr--r-- 1 ec2-user ec2-user  27514 Jan 24 21:15 iompi_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user  14247 Jan 24 21:15 iompi_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user  11798 Jan 24 21:15 ionf_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user   1419 Jan 24 21:15 Makefile.conf.in*
-rwxr--r-- 1 ec2-user ec2-user  56745 Jan 24 21:15 nf_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user 169034 Jan 24 21:15 piodarray.F90*
-rwxr--r-- 1 ec2-user ec2-user  45391 Jan 24 21:15 piodarray.F90.in*
-rwxr--r-- 1 ec2-user ec2-user   2805 Jan 24 21:15 pio.F90*
-rwxr--r-- 1 ec2-user ec2-user   1233 Jan 24 21:15 pio_kinds.F90*
-rwxr--r-- 1 ec2-user ec2-user 100774 Jan 24 21:15 piolib_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user    967 Jan 24 21:15 pio_mpi_utils.F90*
-rwxr--r-- 1 ec2-user ec2-user  14959 Jan 24 21:15 pio_msg_callbacks.F90*
-rwxr--r-- 1 ec2-user ec2-user  47285 Jan 24 21:15 pio_msg_getput_callbacks.F90*
-rwxr--r-- 1 ec2-user ec2-user  12835 Jan 24 21:15 pio_msg_getput_callbacks.F90.in*
-rwxr--r-- 1 ec2-user ec2-user  14264 Jan 24 21:15 pio_msg_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user  54688 Jan 24 21:15 pionfatt_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user  16696 Jan 24 21:15 pionfatt_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user 233894 Jan 24 21:15 pionfget_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user  16075 Jan 24 21:15 pionfget_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user 219454 Jan 24 21:15 pionfput_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user  28369 Jan 24 21:15 pionfput_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user  20231 Jan 24 21:15 pionfread_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user   6809 Jan 24 21:15 pionfread_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user   3496 Jan 24 21:15 pio_nf_utils.F90*
-rwxr--r-- 1 ec2-user ec2-user  26547 Jan 24 21:15 pionfwrite_mod.F90*
-rwxr--r-- 1 ec2-user ec2-user   8991 Jan 24 21:15 pionfwrite_mod.F90.in*
-rwxr--r-- 1 ec2-user ec2-user  74039 Jan 24 21:15 pio_spmd_utils.F90*
-rwxr--r-- 1 ec2-user ec2-user  19461 Jan 24 21:15 pio_spmd_utils.F90.in*
-rwxr--r-- 1 ec2-user ec2-user  17487 Jan 24 21:15 pio_support.F90*
-rwxr--r-- 1 ec2-user ec2-user  14136 Jan 24 21:15 pio_types.F90*
-rwxr--r-- 1 ec2-user ec2-user   3202 Jan 24 21:15 pio_utils.F90*
-rwxr--r-- 1 ec2-user ec2-user   7416 Jan 24 21:15 piovdc.F90*
-rwxr--r-- 1 ec2-user ec2-user   1180 Jan 24 21:15 README.config*
-rwxr--r-- 1 ec2-user ec2-user   8949 Jan 24 21:15 rearrange.F90*
-rwxr--r-- 1 ec2-user ec2-user   4298 Jan 24 21:15 rearrange.F90.in*
drwxrwxr-x 4 ec2-user ec2-user   4096 Jan 24 21:15 .svn/
-rwxr--r-- 1 ec2-user ec2-user  14889 Jan 24 21:15 topology.c*

AER_GM

gmodica@...

...Also independently checked out the pio library from github (https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio). The configure file is not in that repository--GM

AER_GM

pokhotelov@...

Does anybody know if the pio distribution in this repository is correct? I downloaded the code by changing svn repositories from parallelio to github, as suggested, and I can´t build CESM. I am getting multiple errors about undefined references in pio libraries (see log attached)

 

Attachment: 
r.e.bartlett@...

Was the pio issue resolved?

I have a functioning installation of CESM1.2.2 which I created in September 2016 and which used the repository changes above. Cases build and run successfully in this installation.

However, I am now trying to set up CESM1.2.1 (for compatibility with some customised compsets a colleague is hoping to use) and am having the same error with buildlib.pio as gmodica details above.

Any help would be much appreciated. Thanks.

jedwards

PIO was moved from a autoconf based build to a cmake based build after pio1_7_2 - if you need the older autoconf based build you should use

       https://github.com/NCAR/ParallelIO.git/tags/pio1_7_2/pio

 

CESM Software Engineer

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