Segmentation fault using era52arl

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chegch
Posts: 3
Joined: January 18th, 2020, 1:41 pm
Registered HYSPLIT User: No

Re: Segmentation fault using era52arl

Post by chegch »

Hi
Have you got this solved? I also have the same error and I'm on physical linux machine (HPC). The data is also downloaded by using hysplit_metdata. The error message is below:

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Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7F137AB5F697
#1  0x7F137AB5FCDE
#2  0x7F137A4AD27F
#3  0x7F137B300F77
#4  0x7F137B304244
#5  0x405DD5 in MAIN__ at era52arl.f:648
Segmentation fault
It seems the line 648 in era52arl.f is not working properly, which is

Code: Select all

call grib_get(igrib(i),'gridType',project)
. Then I tested the grib_get by just

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>grib_get test ERA5_2017.Sep01.2dpl.all.grib
, and it didn't give me any error message. I also tried to allocate memory up to 40GB (with PBS), but this error still exists.

The example data I used can be found in here

Many thanks!
HC
chegch
Posts: 3
Joined: January 18th, 2020, 1:41 pm
Registered HYSPLIT User: No

Re: Segmentation fault using era52arl

Post by chegch »

Hi

Did you figure out this error? I got this error too when converting ERA5 data, and I'm on a physical Linux machine.
I even tried to download a sample data for just one day, but still showed this error. Maybe it has something to do with the eccodes?
The error message is below

Code: Select all

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0  0x7F137AB5F697
#1  0x7F137AB5FCDE
#2  0x7F137A4AD27F
#3  0x7F137B300F77
#4  0x7F137B304244
#5  0x405DD5 in MAIN__ at era52arl.f:648
Segmentation fault
:


Many thanks
HC
AlexB
Posts: 7
Joined: September 26th, 2019, 10:04 am
Registered HYSPLIT User: Yes

Re: Segmentation fault using era52arl

Post by AlexB »

Hi,

So far, I did not find any solution to this issue. You even have gone further than I have in your search for sources of error.
I will keep you informed through this thread if finally make it and be happy if you do the same in case of successful troubleshooting.

Thanks,

Alex
Xisco
Posts: 1
Joined: February 11th, 2020, 11:01 am
Registered HYSPLIT User: Yes

Re: Segmentation fault using era52arl

Post by Xisco »

Hi everyone,
I also received the same error as AlexB, even the same messages with a dedicated Linux machine (not a virtual machine). Do you know if anyone has made any progress with this?
Thank you very much
Xisco
alicec
Posts: 251
Joined: February 8th, 2016, 12:56 pm
Registered HYSPLIT User: Yes

Re: Segmentation fault using era52arl

Post by alicec »

Please make sure you have the latest version of era52arl.f
I have added the most recent version to the github repository so you may get it from there as well.
https://github.com/amcz/hysplit_metdata

Try using the grib_dump utility with eccodes to see what is in your grib file.
https://confluence.ecmwf.int//display/ECC/GRIB+tools

Alice
nanditha
Posts: 3
Joined: March 6th, 2020, 2:27 pm
Registered HYSPLIT User: Yes

Re: Segmentation fault using era52arl

Post by nanditha »

Hi, I received the same error while I attempted conversion of ERA5 data to arl. I used hysplit 4 version and eccodes 2.18.0, which is the latest for the compilation of era52arl code. I successfully compiled era52arl and executable file got created.
The command used for conversion is
./era52arl -iERA5_2000.Jan01.3dpl.grib -aERA5_2000.Jan01.2dpl.all.grib -v

However, I am receiving segmentaion fault as follows
Existing decoding configuration: era52arl.cfg
Allocating agrib 264 ERA5_2000.Jan01.2dpl.all.grib
Allocating igrib 5328 ERA5_2000.Jan01.3dpl.grib
levels found in 3d file pl
Number of time periods found 24
-35.0000000 15.0000000 60.0000000 135.000000 0.250000000 0.250000000

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f4d8122a2ed in ???
#1 0x7f4d81229503 in ???
#2 0x7f4d808a6fcf in ???
#3 0x7f4d81229a0b in ???
#4 0x7f4d813a85fd in ???
#5 0x7f4d8139616b in ???
#6 0x55d964560697 in ???
#7 0x55d96455c2c9 in era52arl
at /media/nanditha/data2/THESIS/hysplit4/hysplit4/data2arl/era52arl/era52arl.f:829
#8 0x55d964557b32 in main
at /media/nanditha/data2/THESIS/hysplit4/hysplit4/data2arl/era52arl/era52arl.f:102
Segmentation fault (core dumped)

The lines in the era52arl.f corresponding to 102 and 829 are follows
102: use eccodes
829: CALL PAKSET(lunit,ARLCFG_NAME,1,NXP,NYP,NZP)

I have checked my grib file and it is upto date.
I have also checked the dependent library requirements in the exec folder, and I obtained the desired output.
Also the code did not provide any message file or error log, even though I used -v option.

I am using the updated era52arl.f downloaded from the GIThub site.

Thanks in advance if someone could help me out in this regard. I am stuck at this location for a long time.
yaqiang
Posts: 54
Joined: October 5th, 2015, 10:20 pm
Registered HYSPLIT User: Yes

Re: Segmentation fault using era52arl

Post by yaqiang »

You can check this topic for converting ERA5 to ARL data format: viewtopic.php?f=30&t=1778 .
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