installation fails with Intel C++ (ICC) 2021.8.0

[natalie-perlin]

Installing rocoto on a new NCAR/UCAR Derecho, installation fails with the errors:

xmlIO.c(1450): error: identifier "LZMA_OK" is undefined
      ret =  (__libxml2_xzclose((xzFile) context) == LZMA_OK ) ? 0 : -1;
                                                     ^

xmlIO.c(2044): warning #3179: deprecated conversion of string literal to char* (should be const char*)
      char *			content_type = (char *) "text/xml";
            			               ^

xmlIO.c(2044): warning #3179: deprecated conversion of string literal to char* (should be const char*)
      char *			content_type = (char *) "text/xml";
            			               ^

xmlIO.c(2056): warning #3179: deprecated conversion of string literal to char* (should be const char*)
  	content_encoding = (char *) "Content-Encoding: gzip";
  	                   ^

xmlIO.c(2056): warning #3179: deprecated conversion of string literal to char* (should be const char*)
  	content_encoding = (char *) "Content-Encoding: gzip";
  	                 ^

compilation aborted for xmlIO.c (code 2)
make[2]: *** [Makefile:1248: xmlIO.lo] Error 1
make[2]: Leaving directory '/glade/work/epicufsrt/contrib/derecho/rocoto/build/libxml2-2.9.4'
make[1]: *** [Makefile:1440: all-recursive] Error 1
make[1]: Leaving directory '/glade/work/epicufsrt/contrib/derecho/rocoto/build/libxml2-2.9.4'
make: *** [Makefile:859: all] Error 2

Using develop branch of rocoto (version 1.3.3 has the same issues),
compilers: icc (ICC) 2021.8.0 20221119 and icpc (ICC) 2021.8.0 20221119
ruby: ruby 3.1.0p0 installed under /glade/u/apps/derecho/23.06/opt/bin/ruby or
ruby 2.5.9p229 installed under /usr/bin/ruby (same errors result)

Any suggestions on resolving the compile issue?..

[christopherwharrop]

@natalie-perlin - Try building it with Gnu. Other compilers are not needed or supported.

[natalie-perlin]

@christopherwharrop -
using gcc did not seem to help, no intel modules loaded, no craype loaded.
Running as:
./INSTALL --with-ruby=/glade/u/apps/derecho/23.06/opt 2>&1 | tee build.with.ruby.log4

Log file attached build.with.ruby.log4. The error in the end:

...
CC       xmlIO.lo
xmlIO.c: In function ‘xmlXzfileClose’:
xmlIO.c:1450:52: error: ‘LZMA_OK’ undeclared (first use in this function); did you mean ‘Z_OK’?
     ret =  (__libxml2_xzclose((xzFile) context) == LZMA_OK ) ? 0 : -1;
                                                    ^~~~~~~
                                                    Z_OK
xmlIO.c:1450:52: note: each undeclared identifier is reported only once for each function it appears in
make[2]: *** [Makefile:1248: xmlIO.lo] Error 1
make[2]: Leaving directory '/glade/work/epicufsrt/contrib/rocoto/build/libxml2-2.9.4'
make[1]: *** [Makefile:1440: all-recursive] Error 1
make[1]: Leaving directory '/glade/work/epicufsrt/contrib/rocoto/build/libxml2-2.9.4'
make: *** [Makefile:859: all] Error 2

build.with.ruby.log4.txt

[natalie-perlin]

On other systems (NOAA cloud platforms), rocoto install with the standard /usr/bin/ruby also fails with the following:

...
libxml-ruby-3.0.0/test/test_suite.rb
/bin/ruby extconf.rb --with-xml2-lib=/contrib/EPIC/rocoto/lib/libxml2/lib --with-xml2-include=/contrib/EPIC/rocoto/lib/libxml2/include/libxml2
mkmf.rb can't find header files for ruby at /usr/share/include/ruby.h

Develop branch of rocoto is checked out. Gcc is 4.8.5 20150623 (Red Hat 4.8.5-44)

[SamuelTrahanNOAA]

It sounds like your Ruby installation is incomplete. The Hercules admins somehow installed just the Ruby non-interactive interpreter without any of the header files. It is likely that the NOAA cloud platforms did the same. There's a separate package for Ruby development. It is probably ruby-dev, ruby-devel, or something similar. Installing that should solve your Ruby problem.

Hercules admins fixed it by compiling Ruby and proving a modulefile ruby/3.2.1. If you install Ruby yourself, do it manually, without using Spack. Do not load any modules before compiling. The same goes for Rocoto. Other than the module for a clean build of Ruby, don't have anything else loaded.

[natalie-perlin]

Solution found for Derecho, thanks to @mark-a-potts.
Besides unloading (purging) all the modules and setting GNU compilers, e.g.,
export CC=gcc; export CXX=g++

add "--without-lzma" to the configure line for libxml2 in INSTALL file.

[natalie-perlin]

@SamuelTrahanNOAA - somehow on Hercules, standard ruby install location in /usr/bin/ruby and no special options worked out for installing rocoto.

[christopherwharrop-noaa]

@natalie-perlin - It might be time for an update of the libraries used for Rocoto. Libxml2 probably isn't the only thing that needs updating. With the other typo that was fixed, a new bugfix release is in order as well. Would be good to take care of both at the same time.

[SamuelTrahanNOAA]

somehow on Hercules, standard ruby install location in /usr/bin/ruby and no special options worked out for installing rocoto

Yes, there is an open ticket about that. The solution is:

module load ruby/3.2.1

With that, Rocoto will compile.

EDIT: Also, you do not need to load that module before running Rocoto. It remembers what Ruby was used to compile it.