jellyfish failing to install while building gkno

Question

[brettin]

When installing gnko, it continues to fail when installing jellyfish. I have confirmed that jellyfish will compile and deploy outside of gkno using the standard install instructions for jellyfish and then setting the LD_LIBRARY_PATH=/usr/local/lib.

I am installing on a bare ubuntu image, so it is possible that I'm missing a dependency. Here is what the bootstrap.sh script looks like:

apt-get update
apt-get install -y build-essential
apt-get install -y openjdk-7-jdk
apt-get install -y ant
apt-get install -y git
apt-get install -y cmake
apt-get install -y ruby1.9.1
apt-get install -y libncurses5-dev
apt-get install -y libncurses5
apt-get install -y zlib1g-dev

I tried this because I was unsure if yaggo was installing correctly.

gem install rake
git clone https://github.com/gmarcais/yaggo.git
cd yaggo/
rake gem
gem install ./pkg/yaggo-1.5.4.gem

The installation stops here:

  jellyfish...Traceback (most recent call last):
  File "/home/ubuntu/gkno_launcher/src/gkno.py", line 502, in <module>
    main()
  File "/home/ubuntu/gkno_launcher/src/gkno.py", line 291, in main
    success = admin.run(sys.argv)
  File "/home/ubuntu/gkno_launcher/src/gkno/adminUtils.py", line 84, in run
    if   self.mode == "build"    : success = self.build()
  File "/home/ubuntu/gkno_launcher/src/gkno/adminUtils.py", line 153, in build
    if self.buildTool(tool):
  File "/home/ubuntu/gkno_launcher/src/gkno/adminUtils.py", line 539, in buildTool
    success = tool.build(out, err)
  File "/home/ubuntu/gkno_launcher/src/gkno/conf/gknoTools.py", line 73, in build
    return self.doBuild()
  File "/home/ubuntu/gkno_launcher/src/gkno/conf/gknoTools.py", line 350, in doBuild
    if not self.runCommand("autoreconf -i") : return False
  File "/home/ubuntu/gkno_launcher/src/gkno/conf/gknoTools.py", line 90, in runCommand
    p = subprocess.Popen(command.split(), env=self.environ, stdout=self.out, stderr=self.err)
  File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Here is the err log:

root@precise64:/home/vagrant/gkno_launcher/logs# more build_jellyfish.err 
setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.
---> bin
<--- bin
---> lib
---> lib/yaggo
<--- lib/yaggo
<--- lib
setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.
---> bin
updating shebang: yaggo
updating shebang: create_yaggo_one_file
<--- bin
---> lib
---> lib/yaggo
<--- lib/yaggo
<--- lib
setup.rb:788: Use RbConfig instead of obsolete and deprecated Config.
rm -f InstalledFiles
---> bin
mkdir -p /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/bin
install yaggo /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/bin/
install create_yaggo_one_file /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/bin/
<--- bin
---> lib
mkdir -p /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib
---> lib/yaggo
mkdir -p /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install stub.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install library.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install parser.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install version.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install zsh_completion.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install dsl.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install general.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
install man_page.rb /home/vagrant/gkno_launcher/tools/Jellyfish/yaggo/lib/yaggo
<--- lib/yaggo
<--- lib

and here is the stdout log:

root@precise64:/home/vagrant/gkno_launcher/logs# more build_jellyfish.out 
Cloning into 'yaggo'...

This is why I tried putting the yaggo installation into the bootstrap script.

When I run the ./gkno build again, the remaining tools install, except for jellyfish. The log messages for the jellyfish failure are different, but apparently the failure in this case is not sufficient for the install program to stop. The install program successfully installs the remaining tools.

Any help would be appreciated. I'm working in two environments, both ubuntu, both virtualized, having the same problem with both.

[brettin]

Some additional information. From what I can tell, the call to autoreconf generates a configure file that is not valid. I can replicate this now when building Jellyfish outside of gkno. If autoreconf is run first, then the Jellyfish build fails. If autoreconf is not run, Jellyfish will build. When configure is run, this error is occurring:

./configure: line 15287: syntax error near unexpected token `VALGRIND,'
./configure: line 15287: `      PKG_CHECK_MODULES(VALGRIND, valgrind >= 1.8.0)'

And a bit more information, the call to autoreconf generates this snippet:

libtoolize: `./install-sh' is newer: use `--force' to overwrite

In any case, here is the entire typescript showing two different situations, one using autoreconf and one not using autoreconf. The error is identical to the error message I'm seeing when building Jellyfish from the gkno build command.

Answer 1

[alistairnward]

If you take a fresh clone of gkno and build it, what is the error log from gkno that you get from the Jellyfish failure? Jellyfish is the tool that we've had the most trouble getting to run on most systems, but seems to be running on all the systems we've tested so far. There could be some dependency problem (this was a big problem for Mac installations) - so you definitely need valgrind and automake setup.

We don't want to be setting system level parameters, or requiring users to do additional steps themselves (as far as is possible), so I'd like to see exactly what gkno is seeing as a problem and try and get an integrated solution.

Thanks for the report.

[brettin]

Working with a fresh clone, and a base ubuntu image (precise64), the problem was isolated to the pkg.m4 macro not being installed. This was solved by including pkg-config. Isolated the problem late last night. The resulting bootstrap works now on two different ubuntu builds, The bootstrap looks like this:

#!/usr/bin/env bash
#set up for gnko
apt-get update
apt-get install -y build-essential
apt-get install -y openjdk-7-jdk
apt-get install -y ant
apt-get install -y git
apt-get install -y cmake
apt-get install -y ruby1.9.1
apt-get install -y libncurses5-dev
apt-get install -y libncurses5
apt-get install -y dh-autoreconf
apt-get install -y pkg-config
git clone https://github.com/gkno/gkno_launcher.git
pushd gkno_launcher
./gkno build
popd

[alistairnward]

Ok, thanks for this. I need to go and check on the dependency checking at the start of building gkno. I think I found that pkg-config was also a problem for Mac installations, so we weren't explicitly checking for it. I need to get these updated and then provide instructions on installing all of these dependencies. These reports are very helpful to us, so thank you again.