Installing NMR Software


BioPack

BioPack is installed as a system package in /vnmr and is activated on a per-user basis as needed.
  • A complete BioPack installation only needs to be performed when Varian resets the software to a new base version. Otherwise, you only need to do a BPupdate.
  • Before doing an update, rename the already installed versions of BioPack.tgz and BPupdate.tgz in case you have to recover the previous version, which you know was working.
  • BioPack.tgz and BPupdate.tgz are located in /vnmr/userlib/psglib
  • Follow the installation instructions for doing a system (/vnmr) install

ChemPack

ChemPack is also activated on a per-user basis


Installing Linux

  • Use CDs in bottom rightmost drawer next to 800 CPU. Do not use the CDs that came with the system. Use the homemade CDs containing version
  • Follow the printout “Linux Installation for VnmrJ, rev H1206, located in Varian’s “VnmrJ 2.1B Installation and Administration” manual.

Enable 2nd Ethernet Card

  • get driver file tg3-3.71b-1.src.rpm
  • as root, install the RPM package using
  • # rpm -ivh tg3-3.71b-1.src.rpm
  • cd to the RPM path and build driver for running kernel using
  • # cd /usr/src/redhat
  • # rpmbuild -bb SPECS/tg3.spec
  • install the built package using
  • # rpm -ivh RPMS/x86_64/tg3-3.71b-1.x86_64.rpm
  • The drivers will be installed in /lib/modules//kernel/drivers/net/tg3.ko
  • Load the driver using
  • # insmod t33.ko OR # modprobe tg3

Enable Widescreen LCD Monitor

  • first get driver file NVIDIA-Linux-x86_64-100.14.11-pkg2.run.sh
  • at login screen on CPU
  • press Ctrl-Alt-Backspace
  • login as root (may need to press Alt-F1)
  • kill all processes related to x
  • then kill X
  • answer questions to not debug X
  • sh NVIDIA...
  • then reboot
  • open display->config window
  • select Nvidia Quadro 4 (Genesis)
  • select LCD 1920 x ...
  • logout then login
  • display -> set to 1920 resolution
  • in term window, execute nvidia-xconfig (all as one word)
  • logout then login
  • Use control panel to set nvidia X-server settings:
  • Xserver display config
  • resolution 1920 x 1200
  • color depth=millions
  • Apply
  • save to x-config file


Installing VnmrJ

VnmrJ is relatively stable, but it may be necessary to reinstall VnmrJ if the software becomes corrupted. However, an apparent software problem may actually be caused by a hardware malfunction.

Note: if only one user is having problems, reinitialize that user’s account using vnmrj-admin as when creating a new user.

VnmrJ install
  • use the CDs located in bottom rightmost drawer next to 800 CPU.
  • if this is a reinstall, install into a new directory and use “ln -s” to change /vnmr link to point to different installations.
  • follow the instructions in Varian’s “VnmrJ 2.1B Installation and Administration” manual.