Problems that I experienced with the HPCC

2017-04-21

Many of these issues may be due to me being stubborn with a weird build system. Nonetheless, they were baffling, and I had very little interest in debugging these issues. I just wanted to get my science done after all!

#Module load completely barfs with incomprehensible error

    $ module spider bedtools
    Using system spider cache file
    /opt/software/lmod/bin/lua: /opt/software/lmod/4.1.4icer5/libexec/Spider.lua:662: attempt to perform arithmetic on a nil value
    stack traceback:
        /opt/software/lmod/4.1.4icer5/libexec/Spider.lua:662: in function 'Level1'
        /opt/software/lmod/4.1.4icer5/libexec/Spider.lua:640: in function 'spiderSearch'
        /opt/software/lmod/4.1.4icer5/libexec/lmod:967: in function 'cmd'
        /opt/software/lmod/4.1.4icer5/libexec/lmod:1195: in function 'main'
        /opt/software/lmod/4.1.4icer5/libexec/lmod:1222: in main chunk
        [C]: ?

#Linuxbrew is terribly confused by things that depend on gcc

    brew install hello
    ==> Installing dependencies for hello: glibc, xz, gmp, mpfr, libmpc, isl, gcc
    ==> Installing hello dependency: glibc
    Error: glibc cannot be built with any available compilers.
    Install Clang or brew install gcc

Using module load Clang does not fix problem >_<

#Compiling things manually on software machine does not work on interactive machine

    $ mummer
    Illegal instruction (core dumped)

# Many modules have a secret dependency on loading other modules

    $ module load LASTZ

    Lmod Warning: Did not find: LASTZ

    Try: "module spider LASTZ"
    $ module load GNU
    $ module load LASTZ
    $ lastz
    You must specify a target file
    lastz-- Local Alignment Search Tool, blastZ-like
      (version 1.03.02 released 20110719)
    ...

Etc etc.