build.bash error for upwelling

[marinekame]

Hi all,

I am using Intel Fortran 11.1 20100806 and NetCDF 4.3.3.1 .
When I ran build.bash for upwelling, I got the following error massages.

---(start of messages)---

[mathuser@ENEG02 upwelling]$ ./build.bash > build.bash.log.txt
makefile:239: INCLUDING FILE /home/mathuser/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
makefile:235: INCLUDING FILE /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
ar: creating /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/libUTIL.a
ar: creating /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/libNLM.a
ar: creating /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/libNLM_bio.a
ar: creating /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/libNLM_sed.a
ar: creating /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/libANA.a
ar: creating /home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/Build/libMODS.a
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdf.so: undefined reference to `__intel_sse2_strdup'
/usr/local/src/hdf5-1.8.15_compile/lib/libhdf5.so.10: undefined reference to `__intel_cpu_features_init'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `tbk_string_stack_signal_impl'
/usr/local/src/hdf5-1.8.15_compile/lib/libhdf5.so.10: undefined reference to `__intel_cpu_feature_indicator_x'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strtok'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strncat'
/usr/local/src/hdf5-1.8.15_compile/lib/libhdf5.so.10: undefined reference to `__intel_cpu_feature_indicator'
/usr/local/src/hdf5-1.8.15_compile/lib/libhdf5.so.10: undefined reference to `__intel_cpu_features_init_x'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strcpy'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strchr'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdf.so: undefined reference to `__intel_sse2_strrchr'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strncmp'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `_intel_fast_memmove'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strcat'
/usr/local/src/netcdf-4.3.3.1_compile_intel/lib/libnetcdff.so: undefined reference to `__intel_sse2_strncpy'
/usr/local/src/hdf5-1.8.15_compile/lib/libhdf5.so.10: undefined reference to `__intel_sse2_strcspn'
make: *** [/home/mathuser/work/kameya/RomsRutgers/Projects/upwelling/oceanG] error 1

---(end of messages)---

How should I do to solve the errors ?
How should I rewrite my build.bash ?
I attached my build.bash here.

Thanks.

[kate]

Well, I don't know what's going on. It looks like you are using the intel compiler and that netcdf was compiled with intel. You don't show us the actual link command which failed, though. Did it go into that built.bash.log.txt file? Are you really linking with ifort?

[marinekame]

Hi, kate. Thank you for your reply !
On 1 May, I will show built.bash.log.txt file here from my PC at my workplace.
I'm sorry to keep you waiting.

[marinekame]

Hello, kate.

I'm sorry to have kept you waiting so long.
I attached the built.bash.log.txt file.
Would you please tell me how to solve the problem ?

Thanks.

[kate]

We have ifort with a working netcdf on a system at work. I went to the directory containing the libnetcdf.so file and did:

Code: Select all

chinook01 123% nm libnetcdf.so.11.3.0 | grep strcat
                 U __intel_sse4_strcat

I then went to the intel compiler lib directory and did nm on each lib*.so.5 file with grep to strcat:

Code: Select all

0000000000024820 T __intel_sse2_strcat
000000000002f2c0 T __intel_sse4_strcat
0000000000017950 t __strcat_ichk

is the report from libintlc.so.5. The U from the libnetcdf report means it's an unresolved symbol while the T in the second report shows that the symbol is resolved in that library. The link command should be linking in all relevant intel libraries. The fact that it isn't is something I would get the sys admin for your computer to investigate. If the names don't match exactly between the two libraries (like different underscores or different sse numbers) then you should try recompiling the Netcdf libraries.

[marinekame]

Hello, kate.

Your report was very helpful !
I succeeded in running build.bash.

I added
"export LD_RUN_PATH=${HOME}/lib"
in my build.bash the other day.

And after reading your report, I copied libintlc.so.5 of Intel Composer XE 2015 in
"/usr/local/src/intel/composer_xe_2015.1.133/compiler/lib/intel64"
directory in another Linux machine to
"/home/mathuser/lib"
directory in my Linux machine, in which Intel Compiler 11.1 is installed.
("/home/mathuser" is my home directory, and I copied also libirng.so of Intel
Composer XE 2015 to "/home/mathuser/lib" in my machine the other day.)

Then I succeeded in running build.bash without any errors, and oceanG was created.

Thank you very very much, kate !