Developer

Other Development Pages

Here is a list of other development-related pages. (Some material has been moved because this page is getting very long.)

Topics - Software Projects

• faim development
• vtkMy development

Topics - Platforms

• Development on OS-X
• Development for Linux
• Development on VMS

Topics - Tools

Hardware

Used Alpha stations at http://www.islandco.com

VMS Development

"Hello, world!"

A simple "Hello, world!" application

In C:

Write the following program in your favorite text editor (e.g. eve) and save it as hello.c:

#include <stdio.h>

int main(void)
{
  printf("Hello, world!\n");

  return(0);
}

Compile and link using the following lines:

CC /OBJECT=hello.obj hello.c
LINK hello.obj /EXECUTABLE=hello.exe

Run it:

$ run hello
Hello, world!
$ 

In C++:

Write the following program in your favorite text editor (e.g. eve) and save it as hello.cxx:

#include <iostream>

int main()
{
  cout << "Hello, world!" << endl;

  return 0;
}

Compile and link using the following lines:

CXX /OBJECT=hello.obj hello.cxx
CXXLINK hello.obj /EXECUTABLE=hello.exe

Run it:

$ run hello
Hello, world!
$ 

A "Hello, world!" application with parameters

Write the following program in your favorite text editor (e.g. eve) and save it as say_hello.c:

#include <stdlib.h>
#include <stdio.h>

int main(int argc, char *argv[])
{
  if (argc < 2)
  {
    printf("Usage: hello <name>\n");
    exit(0);
  }

  printf("Hello, %s!\n", argv[1]);

  return(0);
}   

Compile and link using the following lines:

CC /OBJECT=say_hello.obj say_hello.c
LINK say_hello.obj /EXECUTABLE=say_hello.exe

Now you need to define a symbol for your executable:

hello :== $DISK1:[DEVEL.FABIO.EXAMPLES.HELLO]SAY_HELLO.EXE

This allows you to run your program by simply calling "hello". You can give it parameters too, Unix style. The mechanism is known in VMS as "defining a foreign command".

Run it:

$ hello
Usage: hello <name>
$ hello Steve
Hello, steve!
$ hello "Steve"
Hello, Steve!
$

Writing a (Unix) Makefile for the say_hello application

Once the application described above is written, type the following into a file named "Makefile"

all: say_hello.exe

clean:
        delete say_hello.exe;*
        delete say_hello.obj;*

say_hello.exe: say_hello.obj
        LINK say_hello.obj /EXECUTABLE=say_hello.exe

say_hello.obj: say_hello.c
        CC /OBJECT=say_hello.obj say_hello.c

IMPORTANT: the space before the commands in the Makefile (i.e. the space before "delete ...", "LINK ...", etc) is a single TAB character.

You can now compile your program by calling "gmake"

$ gmake

I am assuming, of course, that gmake is installed in your system. In the bone lab, gmake is installed in duck.kin.ucalgary.ca.

Developing new IPL commands in C

A short manual on how to develop new IPL commands in C: Download .doc file

Advanced topics

A list of nice things to add to this short tutorial:

• Status of cmake in VMS

Getting started

Editor:

$! Define the editor
$ eve == "spawn/nowait edit/display=decwindows/tpu"
$ eve filename.txt

Compiler:

$! Define the compiler
$ C64 :== CC/POINTER_SIZE=64/check=pointer=all/optimize=(tune=ev6,level=5)

$! Compile the program 'ipl_scanco_c' and link it to existing libraries
$ c64 ipl:ipl_scanco_c
$!
$ link /exe=ipl:ipl_SCANCO_c -
        ipl:ipl_scanco_c, -
        ipl:ipl_scanco_c_ident/opt, -
        ipl:ipl_proc/lib, -
        ipl:ipl/lib, -
        mu:scanco_ext/lib, -
        dsrc:d3p_scanco/lib, -
        scanco_lib/lib

SCEVA3 (Itanium)

sceva3.ucalgary.ca

Login devel with bone5Rus.

Note that scp is configured to use ssh2 and scp2. Linux (openssh) uses scp1:

http://www.snailbook.com/faq/scp-ossh-to-ssh2.auto.html

Whereas ssh and sftp work out of the box, successfully using scp requires a scp2 client.

SCTHIN (DS10L)

duck.kin.ucalgary.ca has been assigned IP address 136.159.130.33
netmask 255.255.255.0
default router 136.159.130.34
DNS servers 136.159.130.130, 136.159.130.3

Login microct or devel with bone5rus.

To boot into the cluster

>>>boot ewa0

To boot out of the cluster, unplug the ethernet cable and

>>>boot

To get to boot prompt, type shutdown on the login screen. Or, after powerdown, hit ctrl-P repeatedly.

There are two accounts:

• microct
• devel

Installing packages on VMS

Contacts: Piet Schuermans Mark Blanchard

Freeware source

http://h71000.www7.hp.com/freeware/freeware80/

Instructions for unpacking .tar.gz files on VMS

1. Rename the file to file.tgz

2. gunzip file.tgz (creates a file.tar)

3. vmstar file.tar

VMSTAR

A tar program for VMS.

Either install from the source (build it), or apparently the binary can be downloaded from

http://h71000.www7.hp.com/freeware/freeware50/vmstar/alpha/

where you will find VMSTAR.EXE

When extracting files that contain "unix" filenames (e.g., config.h.in), make sure to extract the files with

$ cvstar xof file.tar  ! Option 'o' extracts ODS5 files with ODS2 format

CVS

The sources can be retrieved from http://ftp.gnu.org/non-gnu/cvs/source/stable/

You will need a C compiler on OpenVMS. There are several versions of CVS available, but all of them need some tweaking before they can be successfully built.

cvs-1.11.18 (see build instructions at http://lists.gnu.org/archive/html/bug-cvs/2005-01/msg00280.html)

cvs-1.11.21 (do not use)

cvs-1.11.22 (latest version as of May 26, 2007 -- may be built, but follow instructions as per v.18 above)

Download the .tar.gz file, rename it to .tgz once on vms system, use gunzip then vmstar:

$ rename cvs-1.11.22.tar.gz cvs-1.11.22.tgz
$ gunzip cvs-1.11.22.tgz
$ vmstar xof cvs-1.11.22.tar  ! option 'o' allows ODS2 naming.

For all versions, make the following changes before starting:

1. Before you attempt to compile 1.11.22 or later you will need make a copy of [.LIB]FNMATCH_H.IN as [.LIB]FNMATCH.H

2. Correct typo in [.SRC]BUILD_SRC.COM change "libz" to "zlib"

Note: The directory names would have been cvs-1.11.21.dir on Linux. However VMS doesn't allow more than 1 . in the name. If you enter

$ set process/parse=extended

in a terminal you'll be able to access these files. You rename them (i.e. cvs-1_11_21.dir).

NOTE Piet Schuermans (mailps@mac.com) sent me a binary version of CVS on May 25, 2007 that I am currently using.

USAGE

Note that I have a "getting started on cvs for vms" document that can help.

OpenVMS is case sensitive for passing parameters. So put the parameters between " "

$ cvs -d ":pserver:anonymous@public.kitware.com:/cvsroot/VTK" login
$ cvs -d ":pserver:anonymous@public.kitware.com:/cvsroot/VTK" co "vtknew/CMake"

If your using this repository location frequently then

$ define cvsroot ":pserver:anonymous@public.kitware.com:/cvsroot/VTK"

after this you can skip the -d ...... parameter

$ cvs login
vtk

This will create .cvspass file in your home directory so your only need to use the cvs login once

$ cvs co "vtknew"

public.kitware.com has ip address 66.194.253.19

Update VMS licenses

As user system:

$ lic list/full

and check which licenses are currently from 'MONTAGAR' and expire on Aug 31.

I recommend to only then replace those licenses with the new ones, and not load the whole license text file that you get from HP. Make a 'shortlist' of the licenses you need, then FTP them to the VMS system and copy and paste.

Layered Products (any licence, but NOT the openvms-Alpha itself!)

$ lic del OPENVMS-ALPHA-USER
$ LICENSE REGISTER OPENVMS-ALPHA-USER	-
	/ACTIVITY=CONSTANT=100	-
	/AUTHORIZATION=EDU-711643-12345	-
	/DATE=31-AUG-2007	-
	/ISSUER=MONTAGAR	-
	/PRODUCER=DEC	-
	/TERMINATION=31-AUG-2007	-
	/UNITS=0	-
	/CHECKSUM=1-BBME-NKAP-EAFK-CNCA
$ lic load OPENVMS-ALPHA-USER


$ lic del vmscluster
$ LICENSE REGISTER VMSCLUSTER	-
	/ACTIVITY=CONSTANT=100	-
	/AUTHORIZATION=EDU-711643-12345	-
	/DATE=31-AUG-2007	-
	/ISSUER=MONTAGAR	-
	/PRODUCER=DEC	-
	/TERMINATION=31-AUG-2007	-
	/UNITS=0	-
	/CHECKSUM=1-GOOP-ALPF-PGKG-OBND
$ lic load vmscluster

Then, on SCTHIN, for the basic 'openvms-alpha' license itself. In a cluster, this license must be limited to one computer only, so first, to delete the correct of the multiple openvms-alpha licenses only. If I ever wanted SCTHIN to be the server in a cluster, I should do the following (very unlikely!):

$ lic list openvms-alpha/ful

$ lic delete openvms-alpha/auth=xxxxxx
! after first looking up the authori. of that montagar license.

$ LICENSE REGISTER OPENVMS-ALPHA -
/ISSUER=MONTAGAR -
/AUTHORIZATION=EDU-742405-743161 -
/PRODUCER=DEC -
/UNITS=0 -
/TERMINATION_DATE=31-AUG-2008  -
/ACTIVITY=A -
/OPTIONS=(NO_SHARE) -
/CHECKSUM=2-JMOA-GOFL-AKID-DHCJ

$ lic modify openvms-alpha/auth=EDU-742405-743161/include=scthin
! to make it available to scthin only.

MMS: VMS 'make' tool

To start:

$ mms

An example from Bruno Koller of descrip.mms:

.IGNORE
FFLAGS  = /FAST/OPT=(LEVEL=5,TUNE=EV68,INL=ALL)/OBJECT=$(MMS$TARGET_NAME).OBJ
FGENER  = /ALIGN=(NATURAL,SEQUENCE)/ASSUME=NOACCURACY/OPT=(LEVEL=5,TUNE=GENERIC,INL=ALL)/OBJECT=$(MMS$TARGET_NAME).OBJ_G

.FOR.OBJ
        $(FORT)$(FFLAGS) UD:$(MMS$TARGET_NAME).FOR
        $(FORT)$(FGENER) UD:$(MMS$TARGET_NAME).FOR
.FOR.INC
        $(FORT)$(FFLAGS) UD:$(MMS$TARGET_NAME).FOR
        $(FORT)$(FGENER) UD:$(MMS$TARGET_NAME).FOR

all  :: uct_reconstruction.exe, uct_reconstruction.exe_generic
        write sys$output "UCT_RECONSTRUCTION.EXE generated"

uct_reconstruction.exe :: -
        recoident.opt, -
        uct_reconstruction.obj, -
        scli:uct_reco_constants.inc, -
        calc_fan_beam_angles.obj, -
        rebinning.obj, -
        raw_to_rpro.obj, -
        conereco.obj

        link/exe=uct_reconstruction.exe -
        recoident/opt, -
        uct_reconstruction.obj, -
        calc_fan_beam_angles, -
        rebinning, -
        raw_to_rpro, -
        conereco, -
        scanco_lib/lib

uct_reconstruction.exe_generic :: -
        recoident.opt_g, -
        uct_reconstruction.obj_g, -
        scli:uct_reco_constants.inc, -
        calc_fan_beam_angles.obj_g, -
        raw_to_rpro.obj_g, -
        rebinning.obj_g, -
        conereco.obj_g

        link/exe=uct_reconstruction.exe_generic -
        recoident/opt, -
        uct_reconstruction.obj_g, -
        calc_fan_beam_angles.obj_g, -
        raw_to_rpro.obj_g, -
        rebinning.obj_g, -
        conereco.obj_g, -
        scanco_lib/lib

uct_reconstruction.obj :: ud:uct_reconstruction.for, -
        scli:uct_reco_constants.inc

calc_fan_beam_angles.obj :: ud:calc_fan_beam_angles.for, -
        scli:uct_reco_constants.inc

raw_to_rpro.obj :: ud:raw_to_rpro.for, -
        scli:uct_reco_constants.inc

rebinning.obj :: ud:rebinning.for, -
        scli:uct_reco_constants.inc, -
        scli:ctdata_header_structure.inc

conereco.obj :: ud:conereco.for, -
        scli:uct_reco_constants.inc 

Some notes:

• UD is a logical for user disk search list over different disks, so I can compile on both alpha and vax with just having one source.

• No need to put "ud:" at your site. Also, a few lines may have been wrapped which should be on one line (/fflag...) by the mail program.

• Let me know if you want the mms installation file, you will need the hp campus mms license herefore (which you may already have)

Alternative to MMS: MMK

A free MMS replacement is called Madgoat MMK (http://www.madgoat.com/mmk.html).

Alternative to EVE: NEDIT

NEDIT is also available for VMS and offers a nicer editor, in my opinion (Mark Blanchard).

Online VMS discussion lists

info-vax (comp.os.vms)

SCP hangs and is not working

The problem occured when setting up sceva3 for development. SCP (secure copy) can be used as follows (Linux terminal, untested):

scp Readme.txt devel@sceva3.ucalgary.ca:[.Scratch]

Troubleshooting:

1. Check that all the scripts called from [DEVEL]login.com are present on the machine (alternatively, remove these calls from login.com, but logicals and symbols will not be setup properly, e.g. eve). Errors in the login script will cause scp to hang.

2. If you get: scp1 compatibility mode is not supported. this means that scp on VMS is using ssh2 and scp2 and the client uses scp1 ( http://www.snailbook.com/faq/scp-ossh-to-ssh2.auto.html ). VMS could be configured for scp1, but the better option (Mark Blanchard, Scanco) is to use an scp2 client (is there one for MacosX/Linux? and Windows?).

Linux Machines

Accessing Sodor disk

From Konqueror in KDE, use a path like:

smb://HPL-NT\sboyd@hal/Sodor

XEmacs

Pretty print

• For colour printing, select "Options", "Syntax Highlighting", "In this buffer"
• In "Page Setup" set the margins to be 10 mm on the left and rights sides
• In the "Printer Properties" on the "Effects" tab, use 90% of Normal size

C Shell Scripts

These scripts must be executable.

$ chmod 775 myscript.com

Sample 1

This file aim2voi.com shows the use of command line arguments in a CSH script.

#!/bin/csh
#------------------------------------------------------------------------------
onintr end
if ($#argv < 1) goto usage
#------------------------------------------------------------------------------
aix $1.aim > $1.dsc
aic2voi $1.aim $1.voi
goto end
#------------------------------------------------------------------------------
usage:
#
echo ""
echo "Usage:"
echo ""
echo "aim2voi aim_filename (without aim extension)"
echo "will create a voi and dsc file from an aim"
echo ""
#
exit
#------------------------------------------------------------------------------
end:
exit
#------------------------------------------------------------------------------

Sample 2

Similar to above, but aim2bid.com generates a temporary file called stack which is used as input.

#!/bin/csh
#------------------------------------------------------------------------------
onintr end
if ($#argv < 4) goto usage
#------------------------------------------------------------------------------
set i = $3
while ($i <= $4)
  set nr = $i
  if ($nr<10)  set nr = "0"$nr""
  if ($nr<100) set nr = "0"$nr""
#  if ($nr<1000) set nr = "0"$nr""
  echo "XY" >! stack
  echo "$i" >> stack
  echo "$5" >> stack
  if ($6 != "") then
    echo "0" >> stack
    aio $1 "$2"_"$nr".bid 14 < stack
    convert -size "$7" "$2"_"$nr".bid "$2"_"$nr"."$6"
    \rm -f "$2"_"$nr".bid
  else
    echo "2" >> stack
    aio $1 "$2"_"$nr".bid 14 < stack
  endif
  \rm -f stack
  @ i = $i + 1
end
goto end
#------------------------------------------------------------------------------
usage:
#
echo ""
echo "Usage:"
echo ""
echo "aim2bid aim_filename bid_prefix first_slice last_slice scal_factor [form size])"
echo "                                (values are one-based)              gif/tif/..."
echo ""
#
exit
#------------------------------------------------------------------------------
end:
exit
#------------------------------------------------------------------------------

Sample 3

An example where a sequence of commands are executed resulting in an e-mail to let the user know that their job is finished.

#!/bin/csh
# 
nohup faim -s $1; /bin/csh -cbf "Mail -s 'JOB $1 FINISHED' boyd@kin < ~/adm/mailer/faimjob.txt" &

You would run this script called faim.com as follows

$ faim.com inputfile

Sample 4

This example uses two files. One called wrap.com is the base program that is called in a more general program called wrap_all.com so that many different files can be processed by the base script.

• wrap.com

#!/bin/csh

echo "0" >! stack
echo "0" >> stack
echo "0" >> stack

/home/skb/works/fio/aim_io $1.aim $1_sub.aim minimal 15 < stack

/rm -f stack

exit

• wrap_all.com

#!/bin/csh

~/works/com/wrap calgary_dog_aclx_03-04_med_fem_left
~/works/com/wrap calgary_dog_aclx_03-04_med_fem_right
~/works/com/wrap calgary_dog_aclx_03-04_med_tib_left
~/works/com/wrap calgary_dog_aclx_03-04_med_tib_right

echo "DONE!"
exit

temple.ucalgary.ca

Configuration Details

I include in the attachments my checklist I use for a Solaris 10 installation, adjusted to show only items particular to yours and not my entire decision tree. I added brief explanations for some of the items that might seem arbitrary otherwise.

Very similar decisions are made when installing any release of Linux, Solaris, MS Windows or yet another operating system - the details vary though.

http://docs.sun.com/ has all (too many) the details.

• Operating System Download PDF
• Configuration Download PDF
• Mirror Download PDF
• RAID5 Download PDF
• Finishing Steps Download PDF

Install XEmacs

However, I would not install both Emacs and XEmacs at the same time. Nowadays, I highly recommend installing only one of them, with my preference given to XEmacs. Of course, only when there are no specialized Lisp packages that require Emacs.

Then my installation would be like below:

$ cd /cdrom/s10_software_companion/components/sparc/Packages
$ cat > /tmp/nointeraction
  mail=
  instance=unique
  partial=nocheck
  runlevel=nocheck
  idepend=nocheck
  rdepend=nocheck
  space=quit
  setuid=nocheck
  conflict=quit
  action=nocheck
  basedir=default

$ pkgadd -a /tmp/nointeraction -d . -n SFWbdb SFWgcc34l SFWxmacs
  [ Copyright and legal notices omitted for brevity. ]
  21872 blocks

  Installation of <SFWbdb> was successful.
  [ Copyright and legal notices omitted for brevity. ]
  69953 blocks

  Installation of <SFWgcc34l> was successful.
  [Copyright and legal notices omitted for brevity. ]
  264202 blocks

  Installation of <SFWxmacs> was successful.

$ emacs () { /opt/sfw/bin/xemacs $* ; }

$ pkgadd -a /tmp/nointeraction -d . -n SFWddd SFWgbin SFWgdb
  [ To complete installation of the other packages you require. ]

$ pkginfo SFWbdb SFWddd SFWgbin SFWgcc34l SFWgdb SFWxmacs
  system      SFWbdb    berkeleyDB - Berkeley Database Library
  system      SFWddd    ddd - GNU Data Display Debugger
  system      SFWgbin   binutils - GNU binary utilities
  system      SFWgcc34l gcc-3.4.2 - GNU Compiler Collection Runtime Libraries
  system      SFWgdb    gdb - GNU source level debugger
  system      SFWxmacs  XEmacs - text editor

Developing on Duck

Installing GNV (GNU is not VMS)

Downloading GNV

First, download GNV version 1.9 for VMS 7.3-2
http://h71000.www7.hp.com/opensource/gnv.html

Unzip the file on your workstation. FTP the two .pcsi to duck using the "binary" mode (i.e. type bin before you use get. Make sure that all letters in the file name are uppercase, so, for example, if you got the following after unzipping:

dec-axpvms-gnv-v0109-000-1.pcsi$compressed;1
dec-axpvms-gnv-v0109-000-1.pcsi$compressed_esw;1

rename them to

DEC-AXPVMS-GNV-V0109-000-1.PCSI$COMPRESSED;1
DEC-AXPVMS-GNV-V0109-000-1.PCSI$COMPRESSED_ESW;1

Installing GNV

Login as user system to do the installation.

Follow the installation instructions on http://openvms.compaq.com/OpenSource/gnvreadme_first.html, section 6.

$PRODUCT INSTALL GNV /SOURCE=device:[dir.where.pcsi.are]

Setting up GNV

Follow the installation instructions on http://openvms.compaq.com/OpenSource/gnvreadme_first.html, section 7.
The following modifications were made to configuration files on duck:

1. File SYS$MANAGER:SYSTARTUP_VMS.COM: the following line was added

$ @SYS$STARTUP:GNV$STARTUP.COM

2. File LOGIN.COM at the devel account: added the line below

$ @GNU:[LIB]GNV_SETUP.COM

3. As mentioned in http://openvms.compaq.com/OpenSource/gnvreadme_first.html, section 9.3, long file names are enabled on an ODS-5 disk by adding the follwowing line devel's LOGIN.COM file:

$ SET PROCESS/PARSE_STYLE=EXTENDED

Note that you could also make the terminal case sensitive, but this did not work well, so I did not include this command.

Running GNV

Just start bash:

$ ssh -l devel duck.kin.ucalgary.ca
devel@duck.kin.ucalgary.ca's password: 
Welcome to OpenVMS (TM) Alpha Operating System, Version V7.3-2  

DISK1:[DEVEL]
$ bash
bash$ 

See the list of commands available at http://h71000.www7.hp.com/opensource/gnvreadme_first.html, section 5.