PEP8 Goodness

Plumed

Installing lammps

Verification build
dantopa@darwin-fe2.lanl.gov: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

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64
    ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64
            ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64
            ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64
                            ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64
        ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64
        ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64
    ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64
                ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
        ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64
            ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64
                ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64
                ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64
                        ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64
                            ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64
            ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64

Environment:
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

dantopa@darwin-fe2.lanl.gov: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

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

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.