Problems building SeaDAS

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bruce
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Problems building SeaDAS

by bruce » Tue Apr 07, 2020 2:25 pm America/New_York

following the directions at https://seadas.gsfc.nasa.gov/build_ocssw/, BuildIt completes successfully, but when I get to this step

$ cd $OCSSWROOT/ocssw-src
$ mkdir build
$ cd build
$ cmake ..

cmake fails with

[some lines elided]

-- Found Proj4: /seadas/seadas-7.5.3/ocssw/opt/lib/libproj.so 
-- Found PNG: /seadas/seadas-7.5.3/ocssw/opt/lib/libpng.so (found version "1.6.21")
CMake Error at /usr/share/cmake-3.5/Modules/FindBoost.cmake:1677 (message):
  Unable to find the requested Boost libraries.

  Boost version: 1.60.0

  Boost include path: /seadas/seadas-7.5.3/ocssw/opt/include

  Could not find the following Boost libraries:

          boost_date_time

  Some (but not all) of the required Boost libraries were found.  You may
  need to install these additional Boost libraries.  Alternatively, set
  BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
  to the location of Boost.
Call Stack (most recent call first):
  src/oc/CMakeLists.txt:30 (find_package)

-- Found Intl: /usr/include 
-- Could NOT find Check: Found unsuitable version "", but required is at least "0.9.11" (found CHECK_LIBRARY-NOTFOUND)
-- Could NOT find Valgrind (missing:  VALGRIND_BIN VALGRIND_INCLUDE_DIR)
-- tests/ directory requires Check>=0.9.11, no tests will be built
-- Found Levmar: /seadas/seadas-7.5.3/ocssw/opt/lib/liblevmar.a 

and later on

-- Found SDST: /seadas/seadas-7.5.3/ocssw/opt/lib/libsdst.a 
-- Could NOT find Check: Found unsuitable version "", but required is at least "0.9.10" (found CHECK_LIBRARY-NOTFOUND)
-- tests/ directory requires Check>=0.9.10, no tests will be built
-- Configuring incomplete, errors occurred!

Attached are CmakeOutput.log and CmakeError.log.

Clearly I'm missing a prerequisite but I'm not sure which one...
attachment 1

attachment 2

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bruce
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Problems building SeaDAS

by bruce » Wed Apr 08, 2020 8:17 am America/New_York

PS.  Ubuntu 16.04 up to date as of yesterday.

OB SeaDAS - dshea
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Problems building SeaDAS

by OB SeaDAS - dshea » Wed Apr 08, 2020 9:00 am America/New_York

Looks like we needed to add the date_time module to boost.  Add "date_time" to the build line of:

$OCSSWROOT/opt/src/boost/BuildIt

Make line 25 look like this:

./bootstrap.sh --prefix=$installdir --with-libraries=chrono,filesystem,timer,date_time

Then run the boost/BuildIt script

don

bruce
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Problems building SeaDAS

by bruce » Wed Apr 08, 2020 9:26 am America/New_York

Seems to have fixed the problem.  Thanks!

gnwiii
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Problems building SeaDAS

by gnwiii » Wed Apr 08, 2020 11:48 am America/New_York

A search for "boost date time" should have found an old report with the same solution, but "all's well that ends well".

comachi
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Problems building SeaDAS

by comachi » Mon Apr 13, 2020 11:42 pm America/New_York

Hi. This is quite embarrassing help to ask for.

I lost the permission to write on the external HD I used to work with SeaDAS as well as to delete the files in the trash after an error while running SeaDAS. Although the user has lost its permission to write or delete the files when I check the permission, the system shows that I do have permission wrx as well as the group. The HD is connected via firewire.

I was running SeaDAS 7.5.3 (Ubuntu 18.04.4 LTS) to generate a new virtual band from two dim files: 1: with SeaDAS ocssw generated where the new band was stored and another dim file 2: from mosaic. I saved the .dim file with the new virtual band in the external HD and closed SeaDAS. When I restarted SeaDAS, I reopened the file with the new virtual band but forgot to open the file 2 which the new virtual band is dependent on. Then instead of opening the file 2, I changed the variable from the file 2 in the properties of the new virtual band for a band from file 1 so the virtual band would not need bands from other files. That seemed to work and I tried to save a png image. Then the system didn't allow me to save the file anymore in the external HD. I saved the file in the home but since then I cannot save or overwrite in the external HD nor empty the trash either from the command line or file manager, seadas, etc.

Would somebody help me somehow?
Thanks a lot.
Claudia

gnwiii
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Problems building SeaDAS

by gnwiii » Tue Apr 14, 2020 7:41 am America/New_York

You should assume that the drive may be failing so your data are at risk. Do you have backups?   If not, the first step for a failing drive is to copy as much of the data as possible to a new drive.  You should avoid making any changes to the data on the drive in case it is failing.  Modern drives often fail in a way that preserves most of the data, although it may need some expert guidance to recover the data if the filesystem has been corrupted.

This problem is probably unrelated to SeaDAS.    Firewire is found on older Apple hardware, but rarely on PC hardware.   I happen to have an old PC with a firewire card. Firewire support in Ubuntu 14.04 LTS was not robust.   If your drive is a complete package from a major vendor such as LaCie there may be a support forum specific to that vendor's drives.  The vendor's site may have diagnostic software (but often only available for Windows).  If not, your best bet is to ask for help on one of the forums for Ubuntu users.  If the drive is failing you may need help from linux experts to recover as much of the data as possible.

On the Ubuntu forum you will be asked many questions, so things will go faster if your first post is as complete as possible.

1. Did anything unusual (such as "disk full", "out of space on device", a slowdown, or a power failure) happen before the problem started?

2.  Does the drive work after a reboot?  If the system is dual boot, does the drive work when booted in the other OS?

3. What is the hardware configuration?  Use "sudo lshw" to generate a report that can pasted into a post or attached.  

4. Is the system up to date?  There is no point troubleshooting issues that may have been fixed by an update.

5. What is the output of the "mount" command?    This may show that the external drive has been mounted "read-only".  This can happen if the drive was disconnected while a write operation was in progress or if the drive has failed.

6.  Have you checked the status of the drive and run tests?    The smartmontools package provides the "smartctl" program to use the diagnostics built into modern drives, but not all external drives support it.

comachi
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Problems building SeaDAS

by comachi » Tue Apr 14, 2020 11:58 am America/New_York

Hi, Thank you for your reply.

The HD is external and connected through firewire and has nearly 1 Tbyte free from a total of 3 TBytes.
Answering your questions:
1. The system was slowing down so that's why I tried to save the file where I was working and opened the file (the external HD HD3T). Then, I was not allowed to save it there and I saved it in the home;

2. I restart the system and it didn't allow me to save it in HD3T. I switched it off for a while and restarted again and no way to save or delete files in the HD3T although it shows me that I had permission to write, read and exec in the HD3T.

3. The hardware run wuith memory 3,6 GiB, Intel Core i5 CPU 670@3.47 GHz x 4
Graphics Intel Ironlake Desktop, GNOME 3.28.2 OS type 64-bit, Disk 196,4 GB

I've tried sudo lshw but got only Floating point exception;

4. The system is up to date Ubuntu 18.04.4 LTS.

5. I ran  "mount" and got back:
seadas@buzz:~$ mount
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
udev on /dev type devtmpfs (rw,nosuid,relatime,size=1888388k,nr_inodes=472097,mode=755)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,noexec,relatime,size=382548k,mode=755)
/dev/sda3 on / type ext4 (rw,relatime,errors=remount-ro)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k)
tmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)
cgroup on /sys/fs/cgroup/unified type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate)
cgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,name=systemd)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
cgroup on /sys/fs/cgroup/net_cls,net_prio type cgroup (rw,nosuid,nodev,noexec,relatime,net_cls,net_prio)
cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)
cgroup on /sys/fs/cgroup/rdma type cgroup (rw,nosuid,nodev,noexec,relatime,rdma)
cgroup on /sys/fs/cgroup/perf_event type cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)
cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)
cgroup on /sys/fs/cgroup/memory type cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup on /sys/fs/cgroup/hugetlb type cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)
cgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
mqueue on /dev/mqueue type mqueue (rw,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=35,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=1235)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime,pagesize=2M)
debugfs on /sys/kernel/debug type debugfs (rw,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,relatime)
configfs on /sys/kernel/config type configfs (rw,relatime)
tracefs on /sys/kernel/debug/tracing type tracefs (rw,relatime)
/var/lib/snapd/snaps/gnome-logs_81.snap on /snap/gnome-logs/81 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-system-monitor_135.snap on /snap/gnome-system-monitor/135 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/chromium_1077.snap on /snap/chromium/1077 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gtk-common-themes_1474.snap on /snap/gtk-common-themes/1474 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-calculator_704.snap on /snap/gnome-calculator/704 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-26-1604_98.snap on /snap/gnome-3-26-1604/98 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gtk-common-themes_1440.snap on /snap/gtk-common-themes/1440 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/core_8935.snap on /snap/core/8935 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-characters_495.snap on /snap/gnome-characters/495 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-28-1804_116.snap on /snap/gnome-3-28-1804/116 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-characters_399.snap on /snap/gnome-characters/399 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/chromium_1089.snap on /snap/chromium/1089 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/skype_118.snap on /snap/skype/118 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/core18_1705.snap on /snap/core18/1705 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/core_8689.snap on /snap/core/8689 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-logs_93.snap on /snap/gnome-logs/93 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-calculator_544.snap on /snap/gnome-calculator/544 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/core18_1668.snap on /snap/core18/1668 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-26-1604_97.snap on /snap/gnome-3-26-1604/97 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-28-1804_110.snap on /snap/gnome-3-28-1804/110 type squashfs (ro,nodev,relatime,x-gdu.hide)
/var/lib/snapd/snaps/gnome-system-monitor_127.snap on /snap/gnome-system-monitor/127 type squashfs (ro,nodev,relatime,x-gdu.hide)
/dev/sda5 on /home type ext4 (rw,relatime)
tmpfs on /run/user/121 type tmpfs (rw,nosuid,nodev,relatime,size=382544k,mode=700,uid=121,gid=125)
tmpfs on /run/user/1003 type tmpfs (rw,nosuid,nodev,relatime,size=382544k,mode=700,uid=1003,gid=1003)
gvfsd-fuse on /run/user/1003/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1003,group_id=1003)
/dev/sdb1 on /media/seadas/HD3T type fuseblk (ro,nosuid,nodev,relatime,user_id=0,group_id=0,default_permissions,allow_other,blksize=4096,uhelper=udisks2)

6. I ran "smartctl" and the output was:
seadas@buzz:~$ sudo smartctl -i /dev/sdb1
smartctl 6.6 2016-05-31 r4324 [x86_64-linux-5.3.0-46-generic] (local build)
Copyright (C) 2002-16, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Device Model:     ST3000DM008-2DM166
Serial Number:    Z5032C5W
LU WWN Device Id: 5 000c50 09270525b
Firmware Version: CC26
User Capacity:    xx.xxx.xx.xx.016 bytes [3,00 TB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    7200 rpm
Form Factor:      3.5 inches
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   ACS-2, ACS-3 T13/2161-D revision 3b
SATA Version is:  SATA 3.1, 3.0 Gb/s (current: 3.0 Gb/s)
Local Time is:    Tue Apr 14 10:26:17 2020 -03
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

Then I tried:
seadas@buzz:~$ sudo smartctl -P showall /dev/sdb1
No presets are defined for this drive.  Its identity strings:
MODEL:    /dev/sdb1
FIRMWARE: (any)
do not match any of the known regular expressions.

I guess I should umount it manually in the command line and then mount manually in the command line with permissions to write as well.
I tried:
mount  -t ntfs-3g  -o remount,rw  /dev/sdb1  /media/seadas/HD3T
mount: only root can use "--options" option

So I did:
sudo mount  -t ntfs-3g  -o remount,rw  /dev/sdb1  /media/seadas/HD3T
[sudo] password for seadas:
Remounting is not supported at present. You have to umount volume and then mount it once again.

Would you help me here, please?
Many thanks.
Claudia

gnwiii
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Problems building SeaDAS

by gnwiii » Tue Apr 14, 2020 2:35 pm America/New_York

You seem to have a failed or failing drive.   Manufacturing of modern disk drives has very tight tolerances.   My experience has been that drives often fail soon after the warranty expires, so I now replace them at end-of-warranty.  Out of warranty drives are not to be trusted.

The information in your post would get better help from an Ubuntu forum.   However, three things to note:

There was a bug in lshw caused by a corrupted filesystem.  Try running lshw with the removable drive disconnected.

Systems slowing down can be caused by a failing disk.  Smartctl may confirm this if the hardware supports it.

The line from the mount command:
/dev/sdb1 on /media/seadas/HD3T type fuseblk (ro,nosuid,nodev,relatime,user_id=0,group_id=0,default_permissions,allow_other,blksize=4096,uhelper=udisks2)
shows an NTFS drive mounted read-only.   This can indicate that a disk error occurred for the original mount attempt.   If you don't have a backup of the drive you should attempt to make one before trying to repair the drive.   Repairs to NTFS filesystems are best done using Windows.

comachi
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Problems building SeaDAS

by comachi » Tue Apr 14, 2020 2:39 pm America/New_York

Hi.

Thank you. I've made backup and will try to repair the drive.  Many thanks.
Claudia

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