Keeping old data alive, building CERNLIB

Updated 28/4/1016 with additional link and clarification

Analysis of the data from the ZEUS experiment was performed using Fortran programs. These used the CERNLIB software libraries and data was stored in structures known as Ntuples.
I used Column-wise Ntuples, which are saved in a binary format. So when at the end of my Ph.D. analysis, I saved the old Ntuples to 11 CDs these became largely useless immediately I left Physics.
The Digital dark age therefore came to me sooner than I anticipated.
Fortunately with the source being made freely available and the necessary compilers being included in gcc I thought I'd have a try at building these on my Linux laptop.
At the time of this exercise I was running version 11.10 of Ubuntu.
Here are the steps I took, based on instructions from this page. One major issue I had with Lubuntu was that many of the dependency packages were not installed and I had to discover and apt-get them all. For this reason it's better not to try this on a cut down Linux.

• Install gfortran (this is part of gcc, I have version 4.6.3)
• Copy and unpack the CERNLIB binaries
• Because I had a cut down Linux, I needed to build LessTif
• Get xutils-dev package for imake
• Set up the  build environment
   cd to the cern folder
   ~$ export CERN_ROOT=CERN_PATH/VERSION
   ~$export CVSCOSRC=$CERN_ROOT/src
   ~$mkdir$CERN_ROOT/build
   ~$cd$CERN_ROOT/build
   ~$export PATH=$CERN_ROOT/bin;$PATH

• Update $CVSCOSRC/config/linuc.cf This file has some operating system specific information, I changed the following
  • #define hasgfortran
  • Change CcCmd to gcc
  • Check #define X11Includes
    This needs to point to the location of the X Window headers, these can be installed using

    sudo apt-get install xserver-xorg-dev

• Run $CVSCOSRC/config/imake_boot to create the Makefile from the imake files
• Run gmake bin/kuipc to build kuipc – this is built to /cern/new/bin
• Add kuipc to path because this is required for the next build
• Run gmake 

When I finally succeeded I was able to write a simple Fortran program that was able to load my old ntuple files.

A couple of other tips

link gmake to make using sudo ln -s /usr/bin/make /usr/bin/gmake

 

Problems and errors

There were a couple of errors in the main build that needed fixing:

#1

Conflicting types for _XmDrawShadow /usr/local/include/xm/DrawP/h Previous declaration is obsolete

Fix: Remove _XmDrawShadow(); from iconwidget.c

 
#2

Pawlib/paw/cpaw/bugrep.c L_cuserid undeclared.

Fix: It should be in <stdio.h> but add #define L_cuserid 9 in the file

Finally, Liblapack3.a is required for PawX11

Fix: Download and build BLAS & LAPAC

Of course now in 2015, CERNLIB is available from the Ubuntu software manager.

Linux on a new Dell Laptop

I've now got a new Dell Inspiron Laptop (Woo hoo!) and decided to set it up to dual boot Linux and Windows 10.

This post is really for my own reference and benefit, although lessons learnt may well be more widely useful.

Installation

I decided to install Linux Mint with Cinnamon. This was really quite painless.

The drive has approx 1.8 TB of useable space, so I shrunk the Windows C: drive to just over 1TB leaving about 750GB for Mint.

To do this, I entered Disk Management into the windows search box which matched with "Create and Format hard disk partitions" as best match.

Open up this tool, right click on the C:\ drive and select Shrink Volume...

I also needed to disable secure boot in the BIOS. This was easy, simply restart the machine hit F2 on start-up. Then when the BIOS configuration screen appears, navigate to Secure Boot and check disable.

I'd previously created a Linux Mint DVD from the Linux mint downloads page. To boot the Linux disk, restart and hit F12 on start-up.

This should start the LiveCD version which has a desktop icon to install. Double click on this and start the installation.

The important point comes when you are prompted to select the Installation type. At this point check "Something else"

You now enter the screen to manage partitions, select the free space from the earlier shrink and click on +
You will be presented with a dialog to configure the partitions, I created 3 (Repeat the process in this order)

• 50GB Logical for the Linux core, Root : '/'
• 690 GB Logical for Root: 'home/'
• The remainder for Swap, about 7GB

Then run the install. This asked for a few configuration settings, for example Wifi login and language settings. Wait about 15 minutes and finally reboot.

The last thing I did was to run sudo-apt get update and sudo apt-get upgrade to bring the packages up to date.

Video driver

My graphics card is an AMD Radeon R5 M335. This seems to have been released in October 2015 and at the time of writing there were no proprietary Linux drivers for this.

The open source AMD driver doesn't seem to handle the card either. I get the following pop-up on the desktop and errors are shown in the logs (obtained using the dmesg command)



dmesg | grep drm

returns the following

[    1.759698] [drm] Radeon Display Connectors
[    1.759763] [drm] Cannot find any crtc or sizes - going 1024x768
[    1.761755] [drm] fb mappable at 0xC0242000
[    1.761756] [drm] vram apper at 0xC0000000
[    1.761757] [drm] size 3145728
[    1.761758] [drm] fb depth is 24
[    1.761758] [drm]    pitch is 4096
[    1.761942] radeon 0000:01:00.0: fb1: radeondrmfb frame buffer device
[    1.796379] [drm:si_dpm_set_power_state] *ERROR* si_upload_sw_state failed
[    1.796420] [drm] Initialized radeon 2.39.0 20080528 for 0000:01:00.0 on minor 0
[   21.908902] [drm] probing gen 2 caps for device 8086:9d10 = 1724843/e
[   21.908908] [drm] PCIE gen 3 link speeds already enabled
[   21.911907] [drm] PCIE GART of 1024M enabled (table at 0x0000000000040000).
[   22.488470] [drm:r600_ring_test] *ERROR* radeon: ring 0 test failed (scratch(0x850C)=0xCAFEDEAD)
[   22.488474] [drm:si_resume] *ERROR* si startup failed on resume
[   22.489091] [drm:si_dpm_set_power_state] *ERROR* si_upload_sw_state failed

But Linux is reverting to Intel graphics

lspci  | grep VGA returns  00:02.0 VGA compatible controller: Intel Corporation Device 1916 (rev 07)

The machine seems to be working well at the moment so I'm not too worried about this. (I'm not interested in heavy graphics work on this machine) I'll keep a look out for news and will post any updates I see to this page.