After update, problems with the webpage

Help
2011-10-28
2012-06-15
  • Hoai Nguyen
    Hoai Nguyen
    2011-10-28

    Hi Aaron

    its me again!

    • Update Huygens 3.7 to4.1
    • Update Hrm 1.2xx to 2.02

    fix hrm_server_config.inc / hrm_client_config.inc

    Move both files to config folder

    Update via terminal DB 7 to 8

    Without hrm_client_config.inc the website will not work.

    With hrm_server_config.inc, website work, but only Login screen or
    registration screen working.

    But after press enter I get a blank screen!

    Logfiles looks good.

    So I need your help! I don`t find the problems. :(

    Best Hoai

     
  • Aaron Ponti
    Aaron Ponti
    2011-10-28

    Could you please check the configuration files as explained on http
    ://huygens-rm.org/home/?q=node/5
    ? Some
    variables were added in version 2.0 with respect to 1.2.x.

    Short: start a console, change to the 'resources' subfolder in the hrm
    installation directory (let's assume it is /var/www/hrm/resources) and type
    (adapt the paths if needed):

    php checkConfig.php /var/www/hrm/config/hrm_server_config.inc

    and

    php checkConfig.php /var/www/hrm/config/hrm_client_config.inc

    Fix whatever turns out to be incorrect. (Do not forget to restart the queue
    manager).

    Alternatively, you can also take a look at the apache2 error log (cat
    /var/log/apache2/error.log).

    Hope this helps.

     
  • Hoai Nguyen
    Hoai Nguyen
    2011-10-31

    php checkConfig.php /var/www/hrm/config/hrm_server_config.inc

    php checkConfig.php /var/www/hrm/config/hrm_config_config.inc

    Both already checked and fixed! Files ist valid.

    Restart hrmd and reboot server same problem.

    Nothing in the error_log (redhat 5) and access-log i can see that my computer
    is log to teh Server.

     
  • Aaron Ponti
    Aaron Ponti
    2011-10-31

    So, the variables are all there. Have you put some invalid value somewhere?

    If you get a blank page after login, something is broken and some error should
    show up somewhere. Does the browser console say anything? Can you crank up the
    error reporting in php.ini (to E_ALL); or add

    error_reporting(E_ALL);

    or alternatively:

    ini_set('error_reporting', E_ALL);

    at the beginning of home.php?

     
  • Hoai Nguyen
    Hoai Nguyen
    2011-10-31

    I try to make a new hrm_cleint_config.inc and server_config, same problem.

    But now the logfile creat some msg that I can see what the problem could be.

    The scripts try to get the files hrm_client/server_config.inc at
    /var/www/html/hrm/inc/ or somewhere else.

    Have I set something new in hrm.conf?

    Here my Logfile:

    File does not exist: /var/www/html/favicon.ico

    Directory index forbidden by Options directive: /var/www/html/

    Directory index forbidden by Options directive: /var/www/html/

    PHP Warning:
    require_once(/var/www/html/hrm/inc/../config/hrm_client_config.inc) : failed
    to open stream: No such file or directory in
    /var/www/html/hrm/inc/hrm_config.inc on line 17, referer: http://www.zmb.uzh.
    ch/resources/imageprocessing.html

    PHP Fatal error: require_once() : Failed opening required
    '/var/www/html/hrm/inc/../config/hrm_client_config.inc'
    (include_path='.:/usr/share/pear:/usr/share/php') in
    /var/www/html/hrm/inc/hrm_config.inc on line 17, referer: http://www.zmb.uzh.
    ch/resources/imageprocessing.html

    PHP Fatal error: Call to undefined function filter_var() in
    /var/www/html/hrm/inc/Validator.inc on line 43, referer:
    http://130.60.40.64/hrm/

     
  • Aaron Ponti
    Aaron Ponti
    2011-10-31

    You seem to have at least 2 problems:

    1) Apache seems to be preventing access to the config subfolder. Check your
    access directives (in the site configuration).

    2) You are running an old PHP version. HRM needs PHP 5.2 or newer to run (this
    is the "Call to undefined function filter_var()..." error).

     
  • Ok, now it works

    1) Fixed folder access

    2) Fixed php 5.1.6 to 5.2.xx

    Now it working normal, thx for your help.

    :)

     
  • Oh, there is somewhere else another failer

    All jobs finished with an error.

    • HUYGENS ERROR REPORT (stderr) --------------

    Skipping log file creation


    Local time 2011-11-02 15:26:33

    Found a valid license.

    Error when processing template
    /huygens/data/nvh/huygens_src/.hrm_4eb153180c660.tcl

    Local time 2011-11-02 15:26:34

    • HUYGENS REPORT (stdout) --------------------

    19592

    Running /usr/local/svi/bin/hucore.bin

    HomePath predefined /usr/local/svi/

    Looking for Tcl in /usr/local/svi/tcl/lib/tcl8.5...

    Tcl version 8.5.4 type 2.

    Huygens Core 4.1.0p3 initializing Compute Engine 4.1.0p3...

    The system ID is 77bf-c786-6987-5e99.

    Launching task 0 for client 0, ID: 0 on cpu group 0 Setting export option type
    to ics Setting export option multidir to 0 Setting export option cmode to
    scale Requesting 8 threads.

    Init complete

    Doing sub task imgOpen...

    File read series mode: off

    PARAMETER VALUE CHANNEL SOURCE

    • TEMPLATE ----------------------------

    What follows is the Huygens Core template executed when the error occured:

    info {title {Batch processing template} version 2.2 templateName
    batch_2011-11-02_03-26-46 date {Wed Nov 2 15:26:46 CET 2011}} taskList {setEnv
    taskID:0} setEnv {resultDir {/huygens/data/nvh/huygens_dst} perJobThreadCnt
    auto concurrentJobCnt 1 OMP_DYNAMIC 1 timeOut 10000 exportFormat {type ics
    multidir 0 cmode scale}}

    taskID:0 {info {state readyToRun tag {setp microscopicTemplate decon
    deconvolutionTemplate} timeStartAbs 1320244006 timeOut 10000 userDefConfidence
    nometadata} taskList {imgOpen setp adjbl qmle:0 qmle:1 previewGen:0
    previewGen:1 previewGen:2 previewGen:3 previewGen:4 previewGen:5 previewGen:6
    previewGen:7 previewGen:8 previewGen:9 previewGen:10 previewGen:11 imgSave}
    imgOpen {path {/huygens/data/nvh/huygens_src/Elisabeth20x_Series003.part.ics}
    series off index 0} setp {completeChanCnt 2 micr {confocal confocal}
    parState,micr {verified verified} s {0.01 0.01 0 1} parState,s {verified
    verified verified verified} iFacePrim 0 prState,iFacePrim verified iFaceScnd 0
    prState,iFaceScnd verified pr {100 100} parState,pr {verified verified}
    imagingDir {upward upward} parState,imagingDir {verified verified} ps {}
    parState,ps {verified verified} objQuality {good good} parState,objQuality
    {verified verified} pcnt {1 1} parState,pcnt {verified verified} ex {420 520}
    parState,ex {verifie!

    d verified} em {420 522} parState,em {verified verified} exBeamFill {2 2}
    parState,exBeamFill {verified verified} ri {1.47 1.47} parState,ri {verified
    verified} ril {1.515 1.515} parState,ril {verified verified} na {0.14 0.14}
    parState,na {verified verified}} adjbl {enabled 0 ni 0} qmle:0 {q 0.1 brMode
    one it 40 bgMode auto bg 0 sn fair blMode auto pad auto psfMode auto psfPath
    {} timeOut 36000 itMode auto} qmle:1 {q 0.1 brMode one it 40 bgMode auto bg 0
    sn fair blMode auto pad auto psfMode auto psfPath {} timeOut 36000 itMode
    auto} previewGen:0 {image raw destDir
    {/huygens/data/nvh/huygens_src/hrm_previews} destFile
    {Elisabeth20x_Series003.part.ics} type XYXZ} previewGen:1 {image raw destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {Elisabeth20x_Series003.part.ics} type XYXZ} previewGen:2 {image deconvolved
    destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4eb153180c660_hrm.ics} type XYXZ} previewGen:3 {image raw destDir
    {/huygens/data/nvh/huygens!

    _dst/hrm_previews} destFile {4eb153180c660_hrm.ics.original} t!

    ype orth

    oSlice size 400} previewGen:4 {image deconvolved destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile {4eb153180c660_hrm.ics}
    type orthoSlice size 400} previewGen:5 {image deconvolved destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4eb153180c660_hrm.ics.stack} type ZMovie size 300} previewGen:6 {image
    deconvolved destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4eb153180c660_hrm.ics.tSeries} type timeMovie size 300} previewGen:7 {image
    deconvolved destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4eb153180c660_hrm.ics.tSeries.sfp} type timeSFPMovie size 300} previewGen:8
    {image raw destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4eb153180c660_hrm.ics.original.sfp} type SFP} previewGen:9 {image deconvolved
    destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4eb153180c660_hrm.ics.sfp} type SFP} previewGen:10 {destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile {4eb153180c660_hrm.ics}
    type co!

    mpareZStrips size 300} previewGen:11 {destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile {4eb153180c660_hrm.ics}
    type compareTStrips size 300} imgSave {rootName
    {Elisabeth20x_Series003.part_4eb153180c660_hrm}}}


     
  • Hoai Nguyen
    Hoai Nguyen
    2011-11-09

    Hi Aarpon

    you mean this two?

    1) Apache seems to be preventing access to the config subfolder. Check your
    access directives (in the site configuration).

    • I fixed after I check the folder security access, or do you mean there is a failure in the config file?

    2) You are running an old PHP version. HRM needs PHP 5.2 or newer to run (this
    is the "Call to undefined function filter_var()..." error).

    • Update to 5.2xx version, and the Website working again.

    But now I always get this error message, if I start a job.

     
  • Hoai Nguyen
    Hoai Nguyen
    2011-11-10

    Ok, Update to HRM 2.03

    But I still get the Error message.

    This is a mail generated automatically by the Huygens Remote Manager.

    Sorry, the processing of the image

    Elisabeth20x_Series003.part.ics

    has been terminated with an error.

    Your job started at 2011-11-10 08:09:28 and failed at 2011-11-10 08:09:34.

    Best regards,

    Huygens Remote Manager

    Job id: 4ebb78a107d39 (pid 10322 on localhost)

    No result file stored in the destination directory.

    • HUYGENS ERROR REPORT (stderr) --------------

    Skipping log file creation


    Local time 2011-11-10 08:09:22

    Found a valid license.

    Error when processing template
    /huygens/data/nvh/huygens_src/.hrm_4ebb78a107d39.tcl

    Local time 2011-11-10 08:09:22

    • HUYGENS REPORT (stdout) --------------------

    10322

    Running /usr/local/svi/bin/hucore.bin

    HomePath predefined /usr/local/svi/

    Looking for Tcl in /usr/local/svi/tcl/lib/tcl8.5...

    Tcl version 8.5.4 type 2.

    Huygens Core 4.1.0p3 initializing Compute Engine 4.1.0p3...

    The system ID is 77bf-c786-6987-5e99.

    Launching task 0 for client 0, ID: 0 on cpu group 0 Setting export option type
    to ics Setting export option multidir to 0 Setting export option cmode to
    scale Requesting 8 threads.

    Init complete

    Doing sub task imgOpen...

    File read series mode: off

    PARAMETER VALUE CHANNEL SOURCE

    • TEMPLATE ----------------------------

    What follows is the Huygens Core template executed when the error occured:

    info {title {Batch processing template} version 2.2 templateName
    batch_2011-11-10_08-09-34 date {Thu Nov 10 8:09:34 CET 2011}} taskList {setEnv
    taskID:0} setEnv {resultDir {/huygens/data/nvh/huygens_dst} perJobThreadCnt
    auto concurrentJobCnt 1 OMP_DYNAMIC 1 timeOut 10000 exportFormat {type ics
    multidir 0 cmode scale}}

    taskID:0 {info {state readyToRun tag {setp microscopicTemplate decon
    deconvolutionTemplate} timeStartAbs 1320908974 timeOut 10000 userDefConfidence
    nometadata} taskList {imgOpen setp adjbl qmle:0 qmle:1 previewGen:0
    previewGen:1 previewGen:2 previewGen:3 previewGen:4 previewGen:5 previewGen:6
    previewGen:7 previewGen:8 previewGen:9 previewGen:10 previewGen:11 imgSave}
    imgOpen {path {/huygens/data/nvh/huygens_src/Elisabeth20x_Series003.part.ics}
    series off index 0} setp {completeChanCnt 2 micr {confocal confocal}
    parState,micr {verified verified} s {0.01 0.01 0 1} parState,s {verified
    verified verified verified} iFacePrim 0 parState,iFacePrim verified iFaceScnd
    0 parState,iFaceScnd verified pr {100 100} parState,pr {verified verified}
    imagingDir {upward upward} parState,imagingDir {verified verified} ps {}
    parState,ps {verified verified} objQuality {good good} parState,objQuality
    {verified verified} pcnt {1 1} parState,pcnt {verified verified} ex {420 520}
    parState,ex {verif!

    ied verified} em {420 522} parState,em {verified verified} exBeamFill {2 2}
    parState,exBeamFill {verified verified} ri {1.47 1.47} parState,ri {verified
    verified} ril {1.515 1.515} parState,ril {verified verified} na {0.14 0.14}
    parState,na {verified verified}} adjbl {enabled 0 ni 0} qmle:0 {q 0.1 brMode
    one it 40 bgMode auto bg 0 sn fair blMode auto pad auto psfMode auto psfPath
    {} timeOut 36000 itMode auto} qmle:1 {q 0.1 brMode one it 40 bgMode auto bg 0
    sn fair blMode auto pad auto psfMode auto psfPath {} timeOut 36000 itMode
    auto} previewGen:0 {image raw destDir
    {/huygens/data/nvh/huygens_src/hrm_previews} destFile
    {Elisabeth20x_Series003.part.ics} type XYXZ} previewGen:1 {image raw destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {Elisabeth20x_Series003.part.ics} type XYXZ} previewGen:2 {image deconvolved
    destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4ebb78a107d39_hrm.ics} type XYXZ} previewGen:3 {image raw destDir
    {/huygens/data/nvh/huyge!

    ns_dst/hrm_previews} destFile {4ebb78a107d39_hrm.ics.original}!

    type or

    thoSlice size 400} previewGen:4 {image deconvolved destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile {4ebb78a107d39_hrm.ics}
    type orthoSlice size 400} previewGen:5 {image deconvolved destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4ebb78a107d39_hrm.ics.stack} type ZMovie size 300} previewGen:6 {image
    deconvolved destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4ebb78a107d39_hrm.ics.tSeries} type timeMovie size 300} previewGen:7 {image
    deconvolved destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4ebb78a107d39_hrm.ics.tSeries.sfp} type timeSFPMovie size 300} previewGen:8
    {image raw destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4ebb78a107d39_hrm.ics.original.sfp} type SFP} previewGen:9 {image deconvolved
    destDir {/huygens/data/nvh/huygens_dst/hrm_previews} destFile
    {4ebb78a107d39_hrm.ics.sfp} type SFP} previewGen:10 {destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile {4ebb78a107d39_hrm.ics}
    type !

    compareZStrips size 300} previewGen:11 {destDir
    {/huygens/data/nvh/huygens_dst/hrm_previews} destFile {4ebb78a107d39_hrm.ics}
    type compareTStrips size 300} imgSave {rootName
    {Elisabeth20x_Series003.part_4ebb78a107d39_hrm}}}


     
  • Aaron Ponti
    Aaron Ponti
    2011-11-10

    Hi,

    I think the best would be for you to send us the file. If you contact me
    directly by email I will give you the info needed for the upload.

    Just a little remark. I couldn't help noticing that the file name is
    Elisabeth20x_Series003.part.ics. Are you sure the file is valid and complete?
    Why is it called .part.ics?

     
  • Hi Aaron

    now it works!

    I try it out with other files and it works. I think my test files are not so
    good. :(

    Thx for your help.

     


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