I have installed NetCDF 4.3.2 and NetCDF-Fortran 4.2. I want to run Community Earth System Model 4.2.
When I create a case, build a case and then run a case, I get the following error:
NetCDF: Invalid dimension ID or name
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011971760 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000012a3c5d0 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011870e20 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011870e20 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011971760 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x00000000129369d0 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x00000000129369d0 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000012a3c5d0 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000012ca7090 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011a16890 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x000000001101a390 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011e02f90 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x00000000123df2b0 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x00000000128e7d30 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000012390540 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011db9ad0 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000012ca7090 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: corrupted double-linked list: 0x0000000012542e90 ***
*** glibc detected *** /home/nitin/CESM/NEW_CASES/CaseX/exeroot/cesm.exe: malloc(): memory corruption: 0x0000000011e5dbb0 ***
What exactly is wrong with the NetCDF installation?
First, don't use CESM to test your netcdf installation. use 'make check'.
Then, the backtrace you provided is pretty clear: you are passing garbage to one of your netcdf routines: probably passing a stack-allocated variable? a missing command line argument? You can get a better answer if you build CESM with debugging: you can then find which netcdf routine is giving you fits.
Related
I am trying to install ruby-2.2 via rvm as required by minitest in my gemfile.lock but I am experiencing an error as shown in the tail of make.log of ruby-2.2 below.
Tail of make.log:
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: arm64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
compiling compar.c
. ./vm_opts.h
compiling complex.c
compiling dir.c
compiling dln_find.c
compiling enum.c
compiling encoding.c
compiling enumerator.c
compiling error.c
encoding.c:825:2: error: implicit declaration of function 'rb_str_change_terminator_length' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
rb_str_change_terminator_length(obj, oldtermlen, termlen);
^
1 error generated.
make: *** [encoding.o] Error 1
make: *** Waiting for unfinished jobs....
+__rvm_make:0> return 2
When I try to install it via rbenv it says:
dgram_write in libcrypto.a(bss_dgram.o)
_RAND_query_egd_bytes in libcrypto.a(rand_egd.o)
...
ld: symbol(s) not found for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [link_a.darwin] Error 1
make[3]: *** [do_darwin-shared] Error 2
make[2]: *** [libcrypto.1.0.0.dylib] Error 2
make[1]: *** [shared] Error 2
make: *** [build_crypto] Error 1
Do upgrade openssl using:
brew upgrade openssl
but it also required me to remove xcode commandlinetools and then reinstall them
sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select --install
I am using ubuntu and when I use bundle install I get an error with nokogiri installation. How can I fix it?
gem_make.out :
At top level:
xslt_stylesheet.c:112:13: warning: ‘swallow_superfluous_xml_errors’ defined but not used [-Wunused-function]
112 | static void swallow_superfluous_xml_errors(void * userdata, xmlErrorPtr error, ...)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1: warning: unrecognized command line option ‘-Wno-self-assign’
cc1: warning: unrecognized command line option ‘-Wno-parentheses-equality’
cc1: warning: unrecognized command line option ‘-Wno-constant-logical-operand’
linking shared-object nokogiri/nokogiri.so
Cleaning files only used during build.
rm -rf /home/domke89/.rvm/gems/ruby-2.7.0/gems/nokogiri-1.10.10/ports/archives
current directory: /home/domke89/.rvm/gems/ruby-2.7.0/gems/nokogiri-1.10.10/ext/nokogiri
make "DESTDIR=" install
make: /usr/bin/mkdir: Command not found
make: *** [Makefile:202: .sitearchdir.-.nokogiri.time] Error 127
make install failed, exit code 2
It seems like a similar question was handled on the Nokogiri Github, on this issue.
From the discussion it seems like you might have some issues with the Ruby and Rubygems configuration on your machine.
I want to install ruby 2.1.3 using this command:
rbenv install 2.1.3
But the result is BUILD FAILED.
I have tried most of the suggestion from Google, but still error. Here is the latest error message:
Last 10 log lines:
make[1]: *** Waiting for unfinished jobs....
compiling psych_to_ruby.c
installing default psych libraries
linking shared-object nkf.so
linking shared-object psych.so
make[2]: Leaving directory '/tmp/ruby-build.20170129014849.4100/ruby-2.1.3/ext/nkf'
make[2]: Leaving directory '/tmp/ruby-build.20170129014849.4100/ruby-2.1.3/ext/psych'
make[1]: Leaving directory '/tmp/ruby-build.20170129014849.4100/ruby-2.1.3'
uncommon.mk:180: recipe for target 'build-ext' failed
make: *** [build-ext] Error 2
I got this error while building open-CV 3.0.0 on Ubuntu 14.04,
[ 86%] Built target opencv_java
make: *** [all] Error 2
I'm on OS X Yosemite and am trying to install fontforge via brew. When I try to install it I get the following error. I'd like to use fontforge to try fontcustom and grunt-webfont. What does this error mean? Do I need to install something else first?
$ brew install fontforge --with-python
==> Downloading https://github.com/fontforge/fontforge/archive/2.0.20140101.tar.gz
Already downloaded: /Library/Caches/Homebrew/fontforge-2.0.20140101.tar.gz
==> ./autogen.sh
==> ./configure --prefix=/usr/local/Cellar/fontforge/2.0.20140101 --without-cairo
==> make
1 error generated.
make[2]: *** [libgdraw_la-gmatrixedit.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
I had exactly the same problem and reinstalling 10.10 XCode Command Line Tools solved it!
:-)
Good luck -