This document can be found at http://www.csb.yale.edu/synchrotron/laptop-userguide.html.

CSB Core Laptop for Synchrotron Trips

Document Version: Wednesday, 13-Aug-2003 12:44:46 EDT

A laptop computer (name: xanthippe) is available for synchrotron trips -- see a CSB staff member for reservations. The laptop serves two functions on these trips.

• At the synchrotron, data can be downloaded to the laptop's accompanying 75GB hard drive, or to additional hard drives purchased by the individual labs. When transported back to CSB, the data can be quickly uploaded from the laptop to the Core computers.
• Data on the laptop can be processed using the HKL2000 suite, during periods when the laptop is not being used for downloading files.

Before you go
Setting up the laptop at the synchrotron
Downloading data to the laptop
Using your own disk(s) with the laptop
Shutting down the laptop
Processing data on the laptop
Packing and transporting the laptop
Using the laptop in the core
Uploading data to the Core servers

Before you go

• A week before your trip, talk to a CSB staff member to reserve the laptop and review procedures. At that time, make sure that you have a user account on the laptop. If not, the staff member must add the account. On a Core computer, as a regular user, type:
  ypcat passwd | grep $user | laptopuser.pl
  Then, on the laptop in its Core configuration, as root, paste the output from the laptopuser command.
• Two days before your trip, pick up the laptop. Test the setup procedure. Make sure you are able to log on. Clean any old files off of /frames. Shut down and pack the laptop.
• Make sure you also bring alternate backup media (whatever tape format is used at your beamline). You should always use at least one additional method (tape, or ftp) to backup your data in addition to the laptop and its hard drive. You should always be prepared to use tape if one of the other methods fails.

In order to use the laptop at the synchrotron, they must provide:

• At least one, and preferably two electrical outlets.
• A few square feet of desk space
• A connection to their network, with DHCP service. (If they allow network connections, the chances are they also provide DHCP service, so don't worry about that).

1. From the main compartment, remove the 2 powercords (one from each side of the disk drive. Remove the orange ethernet patchcord and the silver firewire cable, one from each side of the laptop. Remove the power supplies (from the front partition), the Maxtor disk drive (front partition) and the laptop computer. Remove the mouse, the mouse pad and the short pigtail cables from the front pouch.
2. Plug the mouse into the mouseport in the back of the laptop, all the way on the left side (left is defined facing the laptop from the front).
3. Find the firewire pigtail -- the short, black cable. It has two firewire connections at one end, and a single pcmcia connector at the other. Plug the single pcmcia connector into the firewire card. This is the bottom pcmcia card on the left side of the laptop. The connector tells you which side should face up.
4. The ethernet pigtail is the short, light-colored (white? gray? putty?) cable. with an ethernet connector at one end, and a blue 3Com logo on the other end. Plug the 3Com end into the top pcmcia card on the left side of the laptop, with the logo facing up. Plug either end of the orange ethernet patchcord into the pigtail, and plug the other end into the ethernet jack provided by the synchrotron for network connections. Wrap the red velcro tie around the cable so it does not get lost.
5. Set the Maxtor disk drive on the table. Plug one end of the silver firewire cable into either port at the back of the disk drive (labelled 1394 connection). Plug the other end of the firewire cable into either of the ports at the wide end of the black firrewire pigtail connected to the laptop. Wrap the red velcro tie around the cable so it does not get lost.
   NOTE: Attaching the disk before booting the laptop is optional. See below.
6. Find the rectangular black power supply with the Maxtor Disk label on top and the Rexon label on the bottom. Plug it into the back of the Maxstor disk drive (DC Power In). Using the standard power cord, connect the other end of the power supply to a 110-volt outlet. Save the red velcro tie. The disk drive has no power switch, so connecting it to an outlet should start the disk.
7. Find the rectangular Dell power supply, and connect it to the laptop, at the rear of the left side. Find the Dell power cord. Connect the small end to the power supply, and plug the other end to a 110-volt outlet. Save the red velcro tie.
8. Remove the black security cable and key from the front flap of the carrying case. Secure the laptop, and keep the key in a safe place. Save the red velcro tie.
9. Press the round, black power button on the laptop (left of the Insprion 7000 logo at the top of the keyboard). After normal PC BIOS screens, you will get a RedHat boot screen, offering you the coice of two systems: Synchrotron and Core. Choose the default (Synchrotron) by pressing Enter. If you do nothing, the default system will boot after 20 seconds.
10. The laptop will now proceed to boot the linux system, configured for use at synchrotrons. Eventually, it should present you with a standard logon screen. If one of the green lights on the 3com connector is lit, there is a good chance the network connection has been successfully configured. You'll know for sure when you try to log in.

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Downloading data to the laptop

Before proceding, you should have followed the steps outlined in Setting up the laptop at the synchrotron.

• Log in, using the username taped to the laptop. The password is the name of the conference room on the top floor of the building most of our labs are in. If the conference room was in room 2100 of the Muggle Tower, the password would be 2100muggle.
• If a shell window does not appear, click the shell icon on the bottom of the screen.
• You will want to put your files on the /frames disk (or possibly /frames2 as well; see below. This is the Maxtor FireWire disk connected to the laptop. With the disk attached to the laptop as described above, type:
  > mount /frames
  You must enter this mounting command, even if the disk was attached on startup.
• Create a subdirectory in /frames and cd to it:
  > mkdir -p /frames/username/xtal
  > cd /frames/username/xtal
• (Optional) You can gzip your files on the data collection computers. That will reduce space and download times by about 40%.
• Now, ftp to your data collection computer, and get the frames you need. You can use the mget command to get multiple files; use the prompt command to toggle off being prompted for each filename. Use ftp, not sftp. Download should proceed at about 2.5MB/sec -- about 7 seconds for an 18MB file.
• You should also download any detector calibration files you might need. They will be contained in a subdirectory of $HKLDIR on the synchrotron's data processing computer. On the laptop, they should go into a subdirectory of /usr/local/bin. Create a directory there with a name describing the detector and date, e.g., /usr/local/bin/nsls-x12b-q4-2002.01.11 and use ftp to copy all files from the calibration directory on the synchrotron's computers to the newly-created directory on the laptop.
• (Optional). After transferring your files to /frames on the laptop, you can use gzip to compress them (if you did not do so earlier). For most data formats, gzip will provide a space savings of about 40%.
• Note that, by default, all directories and files you create will have both read and write access from everyone. This will make your life easier later on, so don't change it unless you have a good reason.
• Don't forget to shut down the laptop gracefully when you are done downloading. Don't simply turn off the power.

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Using your own disk with the laptop

You should be able to use your own disk(s) with the laptop, to provide additional storage capacity at the synchrotron, or provide longer-term storage when you get back. We use the Maxtor Personal Storage 3000DV disks, which come in 60-, 80- and 160-GB sizes (costing $280, $310, $400). Order from CDW through the Yale eportal. See the CSB staff for more ordering information.

If you plan to use your own disk(s), please note the following.

• Bring the disk drive to the staff well before your trip. This will enable us to partition the disk, create a filesystem, and verify operation.
• When using your disk with the laptop, you should be able to attach it without shutting down the laptop. If you want to switch disks:
  
  
  • type umount /frames
  • switch disks
  • type mount /frames
  • If things don't work correctly, try turning off the laptop, unplugging the FireWire disk, restarting the laptop, and plugging in the disk. Then attempt mounting again.
  
  
• If you have a very large FireWire disk (e.g., 160GB), the disk may have two partitions on it. If typing "df" indicates that you don't seem to have the full size disk for /frames, try mounting a second partition:
  
  
  • type mount /frames2
  
  Remember to unmount both /frames and /frames2 if it is necessary to unplug the disk.
• Do not attempt to attach two disks at once, even though there are two FireWire ports. Always switch between disks as above.

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Shutting down the laptop

1. If you are logged in to the laptop, log out. (Press the K in the lower left corner of the desktop. From the menu, select the bottom item logout.
2. When the login screen appears, select Shutdown from the lower right corner of the login box. Select Shutdown again from the pop-up box, then OK.
3. The laptop should now shut down gracefully and turn itself off.

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Processing data on the laptop

For arcane reasons, which are explained elsewhere, the laptop must be configured differently for processing data than for downloading data. If you are at the synchrotron, and have just downloaded data, the procedure outlined in this section should put you in data processing mode.

1. If you are logged in to the laptop, log out. (Press the K in the lower left corner of the desktop. From the menu, select the bottom item logout.
2. Then the login screen appears, select Shutdown from the lower right corner of the login box. Select Restart from the pop-up box, then OK.
3. The system will shut down, then restart. Eventually, it will get to the RedHat LILO boot screen, with a choice of booting the Synchrotron or the Core system. Use the down-arrow key (lower-right corner of keyboard) to highlight Core, then press Enter. If you are at a synchrotron, or otherwise not connected to the CSB network, disconnect the ethernet patchcord from laptop as as soon as you press Enter.
4. If all goes well, the system will come up, and you will be presented with the login screen. Log in with the same username and password you used when downloading data.
5. If necessary, click on the shell icon at the bottom of the screen to get a shell window. Go to wherever you have your frames (cd /frames/xxx).
6. You should now be able to invoke denzo, scalepack, or HKL2000. However, HKL2000 will not work (at this writing) because of insufficient memory.
7. Detector calibration files should go in /usr/local/bin/. You should be able to create a directory there and copy the calibration files into that directory. The directory structure and placement for calibration files should be the same as on the processing computer at the synchrotron.

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Packing and transporting the laptop

1. Shut down the laptop (see above).
2. Unlock the laptop security cable. Coil the security cable, secure it with a red velcro tie, and store it in the outside flap of the carrying case.
3. Unplug the power cords from the Maxtor disk and from the laptop.
4. Unplug the mouse from the laptop. Disconnect the orange ethernet patchcord from the pigtail at the laptop and from the network connection. Disconnect the silver firewire cable from the Maxtor disk and from the pigtail at the laptop. Coil the firewire cable and the ethernet patchcord, and secure them with the red velcro ties.
5. Unplug the 3Com pigtail and the firewire pigtail from the pcmcia cards on the left side of the laptop. Do not remove the pcmcia cards.
6. Store the mouse, mousepad and the two pigtails in the front pouch of the carrying case.
7. Close the laptop and place it on end in the rear partition of the main compartment of the carrying case.
8. Place the disk drive in the front partition of the main compartment of the carrying case.
9. Unplug the power supplies for the disk and for the laptop from their power cords. Store the power supplies in the main compartment nex to the disk. Unplug the two power cords from the outlets, coil them and secure them with the red velcro ties. Store them in the main compartment with the disk drive and power supplies. One of them should go next to the disk drive on the outside to provide extra cushoining.
10. Store the orange ethernet patchcord and the silver firewire cable in the main compartment on either side of the laptop.
11. Store these instructions in the zipper compartment on the back of the carrying case.

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Using the laptop in the core and uploading data to Core servers

• Set up the laptop as described above, connecting it to any available ethernet jack in the Core.
• Power on the laptop. When the RedHat LILO prompt appears on the screen, you have a choice of booting the Synchrotron or the Core system. Use the down-arrow key (lower-right corner of keyboard) to highlight Core, then press Enter.
• If all goes well, the system will come up, and you will be presented with the login screen. You may log in with the same username and password you used when downloading data at the synchrotron. But it probably makes more sense to log in with your regular Core username and password (assuming you had the foresight to arrange for an account on the laptop).
• Once the laptop system is up, you have the option of using rlogin or rsh to log onto it from another workstation. You might do this if you don't like using the laptop's keyboard and screen. From another Core computer, type, rlogin xanthippe.
• /srv/frames, /srv/frames2, and /srv/ftpframes should all be mounted on the laptop. To be sure, you may type, for example, mount /srv/frames2 to make sure you can access it.
• You should now be able to transfer your files from /frames (on the laptop) to one of the disks on the Core server. Note you will be copying files from /frames (the local IEEE1394 disk on the laptop) to /srv/frames2 or one of the other frames disks in the Core.
• Under good conditions (nobody else accessing your target frames disk), you should be able to ransfer data at about 3MB/s to /srv/frames2 or /srv/ftpframes, and at 2MB/s to /srv/frames. This translates to 10GB (or 7GB) per hour, or 25-35 seconds for a 75MB frame.
• Alternatively, you can use ftp to upload your files from /frames (on the laptop) to the destination of your choice on darwin or another appropriate Core host. But this will be slower!
• Once your files have been copied to /srv/frames, and safely backed up on tape, it would be polite to remove them from /frames on the laptop.

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