Page History

...

Disk Partitioning

The following table indicates a "standard" suggested disk partitioning for centos7 with a 1 TB SSD.  (Note: the machine, comet2, has 16 GB of RAM.)

Currently recommended partition sizes are in blue.

Here is comet2's current disk config (on a 160 GB HDD):

...

Here is a list of gotchas or concerns that I stumbled into during these project investigations.

...

Absolute NFS file paths will be different.  Using sshfs means every remote file system must have a local mount point.  On central SLAC machines, "/nfs" works.  However, sshfs documentation recommends that mount points be r/w by the user and, usually, /nfs is not such a candidate.  So any scripts or aliases that use the "/nfs" path must be changed. [AFS/YFS is different in that if you elect to have the client installed, the absolute paths will look identical with that on a public SLAC machine.]
** WORKAROUND: On a single-user workstation in the SLAC network, the following example shows how to allow a customary absolute NFS path using a symbolic link:

sudo ln -s /nfs /home/dragon/nfs
mkdir -p /home/dragon/nfs/farm/g/lsst
sshfs dragon@rhel6-64:/nfs/farm/g/lsst /nfs/farm/g/lsst

...

sudo ln -s /afs/slac.stanford.edu/u /u

...

alias person='ssh rhel6-64 person '

...

• At this time (1/7/2020), updating YFS without a concurrent OS kernel update may fail due to an issue with the kmod-yfs library.  The workaround is:

  Code Block
  sudo yum erase kmod-yfs-0.190-1.3.10.0_1062.9.1.el7.x86_64 # (substitute your current version) sudo yum update # or "yum upgrade"

• Tilde (~) does not work.  Remember that LD2.0 machines have their own user databases which are not the same as the SLAC site unix user database.  If you are accustomed to typing "$ ls ~lsstprod/workflows", that will no longer function.  It is not clear how to implement a good, reliable work-around.

• Absolute NFS file paths will be different.  Using sshfs means every remote file system must have a local mount point.  On central SLAC machines, "/nfs" works.  However, sshfs documentation recommends that mount points be r/w by the user and, usually, /nfs is not such a candidate.  So any scripts or aliases that use the "/nfs" path must be changed. [AFS/YFS is different in that if you elect to have the client installed, the absolute paths will look identical with that on a public SLAC machine.]
  ** WORKAROUND: On a single-user workstation in the SLAC network, the following example shows how to allow a customary absolute NFS path using a symbolic link:

  Code Block
  sudo ln -s /nfs /home/dragon/nfs mkdir -p /home/dragon/nfs/farm/g/lsst sshfs dragon@rhel6-64:/nfs/farm/g/lsst /nfs/farm/g/lsst

• Access to AFS home directories can proceed either via an absolute path, e.g., `/afs/slac/u/...` or one can create a symbolic link to recover the familiar `/u/ec/dragon/...` path.
  
  

  Code Block
  sudo ln -s /afs/slac.stanford.edu/u /u

• Lots of SLAC-written and SLAC-specific commands are no longer available locally, e.g., everything in /usr/local/bin
  ** WORKAROUND: Create an alias in your .bashrc to prefix your favorite SLAC command(s) with "ssh rhel6-64 ", e.g.
  
  

  Code Block
  alias person='ssh rhel6-64 person '

• Printing is currently possible via the unix print server, but I've heard rumors that this service might be deprecated and replaced with a Windows-based system.  Also, the current print config in use on comet2 is very rudimentary and needs further thought.  It does not, for example, know about printer-specific functions & capabilities, such as faxing, duplex printing, oddball paper sizes, etc.
  ** FIX: The "BrightQ" print drivers for Canon printers are straight-forward to install, interface seamlessly with CUPS, and offer all the features of my printer (a Canon C5255).  There is a bit of a rigamorole involved (one must "register" twice, once for download and again for installation), but in the end it worked well.  Get the drivers here: https://www.codehost.com/canon/
• Many users will need a moderately-to-highly customized application repertoire to work well for them.  The application list above is acceptable for my (TG) work needs. But there are items that even I need only rarely and it is not clear it is better to seek them out and install locally, or to simply log into a public login machine to use.  Here I am thinking of database tools, advanced development tools, TeX (and friends), more sophisticated printing capabilities, etc.
• While for may activities it is desirable to work locally, one will still need to log onto a public SLAC login machine (think licensed software, certain computing resource management functions, dealing with PPI,  etc.) There are certain files and directories that I would like synchronized between the desktop machine and my SLAC environment (such as ssh keys, personal logbook, app configurations).  Possibly a trscron job would do the trick, but then which copy becomes the master?  I would like a smart synchronizer that allows either environment to make changes that will then be reflected in the other environment.

References

1. SLAC minimum security requirements:
   https://docs.slac.stanford.edu/sites/pub/Publications/701-I02-001-00_Min_Sec_Req_for_Comp.pdf

2. Stanford minimum security requirements:  
   https://uit.stanford.edu/guide/securitystandards

3. SLAC support for Linux:
   Ubuntu/CentOS 7 Desktop Scope of Support

References:

1. SLAC minimum security requirements:
   https://docs.slac.stanford.edu/sites/pub/Publications/701-I02-001-00_Min_Sec_Req_for_Comp.pdf

2. Stanford minimum security requirements:  
   https://uit.stanford.edu/guide/securitystandards

3. SLAC support for Linux:
   Ubuntu/CentOS 7 Desktop Scope of Support

import datetimeimport argparse
## These are the tracts of interest for the end-to-end data settracts = '3636,3637,3638,3639,3830,3831,3832,4028,4029,4030,4229,4230,4231,4232'#tracts = '3636'
## raftIDs are used when converting to/from detector numbersraftIDs = ['R01','R02','R03','R10','R11','R12','R13','R14','R20','R21','R22','R23','R24','R30','R31','R32','R33','R34','R41','R42','R43']
class overlap(object):    ## Table overlap contains: [id,tract,patch,visit,detector,filter,layer]    overlapSQL = "select distinct visit,detector,filter from overlaps where tract in ($1) order by visit,detector;"    #TEST#    overlapSQL = "select distinct * from overlaps order by visit,detector;"
    def __init__(self,dbfile='tract2visit.db',tractList=None):        print("Hello from overlap.init()")        ## Instance variables        self.dbfile = dbfile        self.tractList = tractList        print('dbfile = ',self.dbfile)        print('tractList = ',self.tractList)        self.dbInit = False        return
        def __del__(self):        ## Class destructor         self.con.close()        self.dbInit = False        return
        def initDB(self):        ## Open sqlite3 DB file and create cursor        self.con = sqlite3.connect(self.dbfile)      ## connect to sqlite3 file        self.con.row_factory = sqlite3.Row           ## optimize output format        self.cur = self.con.cursor()                 ## create a 'cursor'        self.dbInit = True        return
    def closeDB(self):        self.con.close()        self.dbInit = False        return
    def stdQuery(self,sql):        if self.dbInit == False: return        print('SQL = ',sql)        ## Perform a query, fetch all results and column headers        result = self.cur.execute(sql)        rows = result.fetchall()   # <-- This is a list of db rows in the result set        ## This will generate a list of column headings (titles) for the result set        titlez = result.description        ## Convert silly 7-tuple title into a single useful value        titles = []        for title in titlez:            titles.append(title[0])            pass        return rows,titles
    def run(self):        self.initDB()
        rows,titles = self.stdQuery(self.overlapSQL.replace('$1',tracts))
        self.closeDB()        return rows, titles
def d2rs(detector):    ## Convert a DM "detector number" to raft/sensor format, e.g.,    ## "R22" "S11"    det = int(detector)    if det > 189 or det < 0: raise Exception("Bad detector number")    raft = int(det/9)    raftID = raftIDs[raft]    s1 = det%9    s2 = int(s1/3)    s3 = s1 % 3    sensorID = f'S{s2}{s3}'    return raftID, sensorID
def rs2d(raftID,sensorID):    # Convert a raft sensor string of form "Rnn" and "Smm" to a DM    # "detector number" (int from 0 to 188)    raft = raftIDs.index(raftID)    det = int(raft)*9+int(sensorID[-2])*3+int(sensorID[-1])    return det
if __name__ == '__main__':
    ## Define defaults    defaultFile = 'tract2visit.db'        ## Parse command line arguments    parser = argparse.ArgumentParser(description='Generate sim file list based on tract overlap')    parser.add_argument('-o','--overlapsFile',default=defaultFile,help='Name of overlap db file (default = %(default)s)')    #    parser.add_argument('-n','--nth',default=0,type=int,help='Desired visit, counting from beginning of sorted list (default=%(default)s)')    parser.add_argument('-v','--version', action='version', version=__version__)    args = parser.parse_args()
    myo = overlap(dbfile='tract2visit.db',tractList=tracts)    rows,titles = myo.run()
    print('table columns = ',titles)    #xtract=titles.index('tract')    xvisit=titles.index('visit')    xdet=titles.index('detector')    xfilt=titles.index('filter')    print('#sensor-visits returned = ',len(rows))    # Sample sim FITS file naming     lsst_a_425529_R14_S00_y.fits    fileList = []    visitList = []    tractList = tracts.split(',')    print(tractList)    n = 0    simpre='/global/projecta/projectdirs/lsst/production/DC2_ImSim/Run2.1.1i/sim/agn-test'    ## Write out a file of sim filenames    vz = open('vizList.txt','w')    for rowz in rows:        n += 1        row = list(rowz)        #print('row = ',row)
        viz = row[xvisit]        if row[xvisit] not in visitList:visitList.append(viz)        rr,ss = d2rs(row[xdet])        file = 'lsst_a_'+str(viz)+'_'+rr+'_'+ss+'_'+str(row[xfilt])+'.fits'        viz8 = f'{viz:08}'        if viz < 445379:            file = os.path.join(simpre,'00385844to00445379',viz8,file)        else:            file = os.path.join(simpre,'00445379to00497969',viz8,file)            pass        vz.write(file+'\n')        fileList.append(file)        if n<20:print(file)        pass
    vz.close()    print('There are ',len(visitList),' visits.')    print('There are ',len(fileList),' files.')
    #/global/projecta/projectdirs/lsst/production/DC2_ImSim/Run2.1.1i/sim/agn-test/00385844to00445379/00425529/lsst_a_425529_R14_S00_y.fits    #/global/projecta/projectdirs/lsst/production/DC2_ImSim/Run2.1.1i/sim/agn-test/00445379to00497969/00457716/lsst_a_457716_R10_S10_i.fits 
    # for file in fileList:    #     print(file)