PEP8 Goodness

Plumed

Installing lammps

Verification build
[email protected]:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5
==> Installing libsigsegv
==> Installing m4
==> Installing pkgconf
==> Installing ncurses
==> Installing readline
==> Installing gdbm
==> Installing perl
==> Installing autoconf
==> Installing automake
==> Installing libtool
==> Installing numactl
==> Installing zlib
==> Installing openssl
==> Installing diffutils
==> Installing bzip2
==> Installing xz
==> Installing libxml2
==> Installing tar
==> Installing gettext
==> Installing help2man
==> Installing bison
==> Installing flex
==> Installing libnl
==> Installing rdma-core
==> Installing ucx
==> Successfully installed ucx
  Fetch: 1.17s.  Build: 40.59s.  Total: 41.76s.
[+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim

[email protected]:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
[email protected]%[email protected] arch=linux-centos7-x86_64
    ^[email protected]%[email protected] patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected] patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected]+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
                    ^[email protected]%[email protected] arch=linux-centos7-x86_64
                        ^[email protected]%[email protected]~symlinks~termlib arch=linux-centos7-x86_64
                            ^[email protected]%[email protected] arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
    ^rdma-core@20%[email protected] build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^[email protected]%[email protected]~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^[email protected]%[email protected]+systemcerts arch=linux-centos7-x86_64
                ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected] arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
                    ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^[email protected]%[email protected]+shared arch=linux-centos7-x86_64
                        ^[email protected]%[email protected]~python arch=linux-centos7-x86_64
                            ^[email protected]%[email protected] arch=linux-centos7-x86_64
                        ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected]+lex arch=linux-centos7-x86_64

Environment:
[email protected]:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

[email protected]:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

[email protected]:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

[email protected]:pr.ucx.spack $ uname -a
Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

[email protected]:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

[email protected]:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <[email protected]>

Whenever attempting to use any ncurses functionality within cscope, a
page fault would result within the ncurses library.

    Program received signal SIGSEGV, Segmentation fault.
    0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    (gdb) bt
    #0  0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    #1  0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6
    #2  0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6
    #3  0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6
    #4  0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
    #5  0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574

This is due to a conflict between libtinfo.so and libtinfow.so. Both are
linked into cscope:

    $ ldd $(which cscope)
    /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash)
        linux-vdso.so.1 (0x00007fff5dbcb000)
        libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000)
        libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000)
        libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000)

Specifically linking libtinfow.so instead of libtinfo.so resolves the
issue.

All instances of '...' above represent the path to the installed ncurses
for Spack.