Error in running mt_prep_snap in Linux

[775747855]

Hi, everyone. I am trying to use the script"mt_prep_snap" but I meet some problem. Please help me .
ubuntu@ubuntu-Precision-3630-Tower:~/Desktop/6TB/bodi/application$ mt_prep_snap 20190314 /home/ubuntu/Desktop/6TB/bodi/application/application/wokdir/PROC/INSAR_b.dim 0.4 3 2 50 200
csh: Input/output error
csh: Trying to start from “/home/ubuntu”
mt_prep_snap Andy Hooper, August 2017

Amplitude Dispersion Threshold: 0.4
Processing 3 patch(es) in range and 2 in azimuth

---

  Segmentation violation detected at 一 12月 02 19:47:41 2019 +0800

---

Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Default Encoding : UTF-8
Deployed : false
Desktop Environment : ubuntu:GNOME
GNU C Library : 2.29 stable
Graphics Driver : Unknown software
MATLAB Architecture : glnxa64
MATLAB Entitlement ID : 5652177
MATLAB Root : /home/ubuntu/soft/matlab
MATLAB Version : 9.5.0.944444 (R2018b)
OpenGL : software
Operating System : Ubuntu 19.04
Process ID : 24954
Processor ID : x86 Family 6 Model 158 Stepping 10, GenuineIntel
Session Key : 64b20a93-480c-46ce-9323-745d1b1de2ce
Static TLS mitigation : Enabled: Full
Window System : No active display

Fault Count: 1

Abnormal termination

Register State (from fault):
RAX = 000000000000000b RBX = 00007f16ef998760
RCX = 787564642e62616c RDX = 00007f16ef998760
RSP = 00007f16ef998430 RBP = 00007f16ef998460
RSI = 0000000000000000 RDI = 00007f16ef998430

R8 = 0000000000000000 R9 = 0000000000000000
R10 = 00000000000000f0 R11 = 00007f171951d5d0
R12 = 00007f16ef998530 R13 = 00007f16ef998ec0
R14 = 00007f16ef998530 R15 = 00007f16e815d6d8

RIP = 00007f1711b36a22 EFL = 0000000000010206

CS = 0033 FS = 0000 GS = 0000

Stack Trace (from fault):
[ 0] 0x00007f1711b36a22 bin/glnxa64/libmwsettingscore.so+00973346 _ZNK8settings4core8Settings21getSettingsByFullNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+00000018
[ 1] 0x00007f16f5bb31e5 bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00725477
[ 2] 0x00007f16f5b830fb bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00528635
[ 3] 0x00007f16f5b6c500 bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00435456
[ 4] 0x00007f16f5b78eca bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00487114
[ 5] 0x00007f16f5b72eaa bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00462506
[ 6] 0x00007f17167cce75 bin/glnxa64/libmwms.so+02625141
[ 7] 0x00007f16f5b72b06 bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00461574
[ 8] 0x00007f171764ec0d /home/ubuntu/soft/matlab/bin/glnxa64/libmwboost_thread.so.1.65.1+00080909
[ 9] 0x00007f1716a77182 /lib/x86_64-linux-gnu/libpthread.so.0+00037250
[ 10] 0x00007f1717da5b1f /lib/x86_64-linux-gnu/libc.so.6+01170207 clone+00000063
[ 11] 0x0000000000000000 +00000000

** This crash report has been saved to disk as /home/ubuntu/matlab_crash_dump.24954-1 **

MATLAB is exiting because of fatal error
Killed
opening /home/ubuntu/Desktop/6TB/bodi/application/application/wokdir/PROC/INSAR_b.dim/rslc/20190206.rslc…
Segmentation fault (core dumped)
8013
2437
mt_extract_cands Andy Hooper, Jan 2007

Patch: PATCH_1
selpsc_patch /home/ubuntu/selpsc.in patch.in pscands.1.ij pscands.1.da mean_amp.flt f 1
file name for zero amplitude PS: pscands.1.ij0
dispersion threshold = 0.4
width = 24039
number of amplitude files = 0
Segmentation fault (core dumped)

psclonlat /home/ubuntu/psclonlat.in pscands.1.ij pscands.1.ll
opening pscands.1.ij…
Error opening file pscands.1.ij

pscdem /home/ubuntu/pscdem.in pscands.1.ij pscands.1.hgt
opening pscands.1.ij…
pscdem: Error opening file pscands.1.ij

pscphase /home/ubuntu/pscphase.in pscands.1.ij pscands.1.ph
opening pscands.1.ij…
Error opening file pscands.1.ij

Patch: PATCH_2
selpsc_patch /home/ubuntu/selpsc.in patch.in pscands.1.ij pscands.1.da mean_amp.flt f 1
file name for zero amplitude PS: pscands.1.ij0
dispersion threshold = 0.4
width = 24039
number of amplitude files = 0
Segmentation fault (core dumped)

psclonlat /home/ubuntu/psclonlat.in pscands.1.ij pscands.1.ll
opening pscands.1.ij…
Error opening file pscands.1.ij

pscdem /home/ubuntu/pscdem.in pscands.1.ij pscands.1.hgt
opening pscands.1.ij…
pscdem: Error opening file pscands.1.ij

pscphase /home/ubuntu/pscphase.in pscands.1.ij pscands.1.ph
opening pscands.1.ij…
Error opening file pscands.1.ij

Patch: PATCH_3
selpsc_patch /home/ubuntu/selpsc.in patch.in pscands.1.ij pscands.1.da mean_amp.flt f 1
file name for zero amplitude PS: pscands.1.ij0
dispersion threshold = 0.4
width = 24039
number of amplitude files = 0
Segmentation fault (core dumped)

psclonlat /home/ubuntu/psclonlat.in pscands.1.ij pscands.1.ll
opening pscands.1.ij…
Error opening file pscands.1.ij

pscdem /home/ubuntu/pscdem.in pscands.1.ij pscands.1.hgt
opening pscands.1.ij…
pscdem: Error opening file pscands.1.ij

pscphase /home/ubuntu/pscphase.in pscands.1.ij pscands.1.ph
opening pscands.1.ij…
Error opening file pscands.1.ij

Patch: PATCH_4
selpsc_patch /home/ubuntu/selpsc.in patch.in pscands.1.ij pscands.1.da mean_amp.flt f 1
file name for zero amplitude PS: pscands.1.ij0
dispersion threshold = 0.4
width = 24039
number of amplitude files = 0
Segmentation fault (core dumped)

psclonlat /home/ubuntu/psclonlat.in pscands.1.ij pscands.1.ll
opening pscands.1.ij…
Error opening file pscands.1.ij

pscdem /home/ubuntu/pscdem.in pscands.1.ij pscands.1.hgt
opening pscands.1.ij…
pscdem: Error opening file pscands.1.ij

pscphase /home/ubuntu/pscphase.in pscands.1.ij pscands.1.ph
opening pscands.1.ij…
Error opening file pscands.1.ij

Patch: PATCH_5
selpsc_patch /home/ubuntu/selpsc.in patch.in pscands.1.ij pscands.1.da mean_amp.flt f 1
file name for zero amplitude PS: pscands.1.ij0
dispersion threshold = 0.4
width = 24039
number of amplitude files = 0
Segmentation fault (core dumped)

psclonlat /home/ubuntu/psclonlat.in pscands.1.ij pscands.1.ll
opening pscands.1.ij…
Error opening file pscands.1.ij

pscdem /home/ubuntu/pscdem.in pscands.1.ij pscands.1.hgt
opening pscands.1.ij…
pscdem: Error opening file pscands.1.ij

pscphase /home/ubuntu/pscphase.in pscands.1.ij pscands.1.ph
opening pscands.1.ij…
Error opening file pscands.1.ij

Patch: PATCH_6
selpsc_patch /home/ubuntu/selpsc.in patch.in pscands.1.ij pscands.1.da mean_amp.flt f 1
file name for zero amplitude PS: pscands.1.ij0
dispersion threshold = 0.4
width = 24039
number of amplitude files = 0
Segmentation fault (core dumped)

psclonlat /home/ubuntu/psclonlat.in pscands.1.ij pscands.1.ll
opening pscands.1.ij…
Error opening file pscands.1.ij

pscdem /home/ubuntu/pscdem.in pscands.1.ij pscands.1.hgt
opening pscands.1.ij…
pscdem: Error opening file pscands.1.ij

pscphase /home/ubuntu/pscphase.in pscands.1.ij pscands.1.ph
opening pscands.1.ij…
Error opening file pscands.1.ij

[Sarto28]

Hi,
I am having the same problem.
How did you solve it?

Thanks

[ABraun]

How many products do you use? Do the interferograms look correct in SNAP?

[Sarto28]

I am using 25 images.

They look fine to me:

By the way, I am using Ubuntu WSL so I cannot understand if the problem is linked to some troubles in Ubuntu.
I am new in SNAP and Linux world.

Thanks

[ABraun]

the problem is that the error message is not very specific. There can be many reasons why the processing does not start as suggested but it’s hard to guess the correct one.

I see you have created a subset from your interferograms. Did you clip the stack of images to the same extent? Both stacsk used for the export must have the same dimensions .

[Sarto28]

Yeah I got it.
It is very difficult to get what is the reason of the error.

I did debursting -> subsetting --> interferogram formation
So the subset stack image has the same dimension of the subset interferogram one.

Thanks

[ABraun]

so we can exclude that as an error source.

How do the interfergrams look like? Have you opened them and checked if they contain valid data?

[Sarto28]

This is my first time with SAR images.
They look fine to me.

[ABraun]

yes, that’s ok for PS InSAR.
I don’t see an error here.

[Sarto28]

And also the PSI export does not give me problem.

There are all the folders to start the mt_prep_snap command

and the Stamps_config should be ok

[szw]

in case you are still in this trouble.

several tips you may check:

1. use csh other than bash. The mt_prep_snap seems not working in bash but go smooth in csh.
2. check if the segmentation error were casued by calamp.c. If it is, then you have to downgrade you gcc and g++ compiler. I did this in fedora 30 with default gcc version 9.2x, the calamp.c program intends to use 4.3.x version. However, I managed to recompile it using gcc-7.4.0 version and that get rid of the segmentation fault.
3. feed mt_prep_snap’s second parameter(data folder) with absolute path, do not use relative path.

I digged these out after 2 weeks of struggling and it seems everthing goes ok so far. I am waiting for the finish of stamps process in matlab:)

[ABraun]

these are good hints, thank you for sharing.

[Naima]

hallo,
do you remember how did you solve your problem, because i have the same and i can not find any solution. if you can to give some advises I will be grateful. Thank you.

[ABraun]

maybe you can report on the suggestions first.
Have you tried using tcsh and launching the StaMPS_Config.tcsh instead?

[Naima]

Dear all,
I tried to work with tcsh but something goes wrong, sometime i can source StaMPS_CONFIG.tcsh but sometimes i got errors , really I don’t know where comes de mistakes. you can see it in the following picture. Thank you for helping me.

[ABraun]

before you can call the StaMPS_CONFIC.tcsh you have to switch to the tcsh console by simply typing tcsh
The commands inside then will be interpreted correctly.

For StaMPS to work properly, you also need triangle.

[Naima]

I did it and I got the same problem.

[ABraun]

it is strange that snaphu is found but the StaMPS scripts not. Are they located in this folder?

The MATLABPATH definiton is strange and somehow differs from the one I expected

Please download StaMPS from here and re-configure the installation and the paths in this file: https://github.com/dbekaert/StaMPS

[Naima]

Dear all,
I installed Stamps from de site (https://github.com/dbekaert/StaMPS), i worked with tcsh but something goes wrong. sometimes tcsh works without fault but sometimes appear a message " MATLABPATH: Undefined variable." well you can see it bellow. mt_prep_snap ran now but i got the same message Segmentation fault (core dumped), the memory of my system is 32Go. Please if you can give some advises where can I look for the solution.

[ABraun]

can you please nagivate one directory upwards (cd …) and then execute the command without the ./ before the path leading to the folder exported from SNAP?