Yambo built was fine but it gives error when running

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? This is the place to look.

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
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(5) the relevant compiler error message

Yambo built was fine but it gives error when running

Postby amirmehdi89 » Thu Apr 19, 2018 12:03 am

Dear Yambo users,

After struggling for a while with compiling Yambo, I was able to compile it properly (it didn't say yambo built failed at the end of it at least). However, I was following this tutorial (hBN) which the calculation seemed to stop and gave the following error, I'm just showing some part of it here:

*** Error in `yambo': free(): invalid pointer: 0x00002aaaaf57ccc0 ***
*** Error in `yambo': double free or corruption (out): 0x00007fffffffac20 ***
*** Error in `yambo': free(): invalid pointer: 0x00002aaaaff81cc0 ***

yambo:18235 terminated with signal 6 at PC=2aaaac80e1f7 SP=2aaaaf379088. Backtrace:

yambo:18235 terminated with signal 6 at PC=2aaaac80e1f7 SP=2aaaafb7d088. Backtrace:

yambo:18235 terminated with signal 6 at PC=2aaaac80e1f7 SP=2aaaafb7d088. Backtrace:

yambo:18235 terminated with signal 6 at PC=2aaaac80e1f7 SP=2aaaafb7d088. Backtrace:

yambo:18235 terminated with signal 6 at PC=2aaaac80e1f7 SP=2aaaafb7d088. Backtrace:
======= Backtrace: =========
/usr/lib64/libc.so.6(gsignal+0x37)[0x2aaaac80e1f7]
/usr/lib64/libc.so.6(+0x7c619)[0x2aaaac855619]
======= Backtrace: =========
/usr/lib64/libc.so.6(abort+0x148)[0x2aaaac80f8e8/usr/lib64/libc.so.6(gsignal]
+0x37)[0x2aaaac80e1f7]
/usr/lib64/libc.so.6(+0x7c619)[0x2aaaac855619]
/usr/lib64/libc.so.6(+0x7c619)[0x2aaaac855619]
/usr/lib64/libc.so.6(+0x74f47)[0x2aaaac84df47]
/usr/lib64/libc.so.6(abort+0x148)[0x2aaaac80f8e8]
/usr/lib64/libc.so.6(gsignal+0x37)[0x2aaaac80e1f7/usr/lib64/libc.so.6]
(gsignal+0x37)[0x/usr/lib64/libc.so.62aaaac80e1f7(gsignal]
+0x37)[0x2aaaac80e1f7]
/usr/lib64/libc.so.6(abort+0x148)[0x2aaaac80f8e8]
/usr/lib64/libc.so.6(+0x7c619)[0x2aaaac855619]
yambo/usr/lib64/libc.so.6(+0x[0x74f47577e09)]
[0x2aaaac84df47]
/usr/lib64/libc.so.6yambo[0x(abort+0x148)[0x2aaaac80f8e8]
/usr/lib64/libc.so.6(clone+0x6d)/usr/lib64/libc.so.6======= Memory map: ========
(abort+0x148)[0x2aaaac80f8e8]
/usr/lib64/libc.so.6(yambo[0x+0x74f47461628]
)
yambo:18235 terminated with signal 6 at PC=2aaaac80e1f7 SP=2aaaaff7f088. Backtrace:
/usr/lib64/libc.so.6(+0x7c619)[0x2aaaac855619]
[0x2aaaac84df47]
/usr/lib64/libc.so.6/usr/lib64/libgomp.so.1((+0x+0x74f47)16435)[0x2aaaabf5b435]
[0x2aaaac84df47]
/usr/lib64/libc.so.6(yambo+0x74f47)[0x2aaaac84df47]
/usr/lib64/libc.so.6yambo[0x577e09]
(+0x7c619)[0x2aaaac855619]
/usr/lib64/libc.so.6(gsignal+0x37)[0x2aaaac80e1f7]
/usr/lib64/libc.so.6(+0x/usr/lib64/libpthread.so.07c619)[0x(+0x2aaaac8556197e25)]
[0x2aaaac5c4e25]
yambo[0x461628]
/usr/lib64/libc.so.6(abort+0x148)[0x2aaaac80f8e8]


My guess is c library issue but I can't track what exactly the problem is. Any help would be thoroughly appreciated. Thank you.
Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Yambo built was fine but it gives error when running

Postby Daniele Varsano » Thu Apr 19, 2018 9:02 am

Dear Amir,
it is not easy to spot the problem for the error message you post.
Can you post the config.log file of your compilation?
Other useful infos:
1) Did yambo write something (produce any file) or just stop immediately with this error?
2) If it do something at which point it stops (in this case please post also report and log file)
3) Are you running in interactive or in batch mode (queue system?)

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: Yambo built was fine but it gives error when running

Postby amirmehdi89 » Thu Apr 19, 2018 2:32 pm

Dear Daniele,
Thank you for your reply. Attached please find the config.log file.

Daniele Varsano wrote:1) Did yambo write something (produce any file) or just stop immediately with this error?

Yambo did produce a couple of files: the report file, the two output files (o.eps..... and o.eel... but they are empty) and this other file that contains pretty much the error that I posted in the last post. One thing I should also mention is that it was showing on the terminal that it was calculating Xo@q[1] |########################################| [100%] but then stopped and gave those errors.

2) If it do something at which point it stops (in this case please post also report and log file)


I think it stopped at calculating Xo@q[1] |########################################| [100%]. I also attached this report file as well.

3) Are you running in interactive or in batch mode (queue system?)


Both. This very last run was on one CPU and it was in interactive mode. But I also did another calculation in batch mode (cluster) and it gave the same type of error.

Thank you very much for your consideration.
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Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Yambo built was fine but it gives error when running

Postby amirmehdi89 » Thu Apr 19, 2018 2:37 pm

For some reason I can't upload the report file. It says "The extension is not allowed." I tried a couple of ways but still doesn't work.
Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Yambo built was fine but it gives error when running

Postby Daniele Varsano » Thu Apr 19, 2018 2:41 pm

Just rename it with an allowed suffix (.log, .txt. , .tar ..etc.).

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: Yambo built was fine but it gives error when running

Postby amirmehdi89 » Thu Apr 19, 2018 2:44 pm

Uploaded!
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Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Yambo built was fine but it gives error when running

Postby Daniele Varsano » Thu Apr 19, 2018 2:47 pm

can you also post your input and your log (standard output)?
In any case, you are linking to libraries that finally for some reason are not used.
Can you try to recompile with just this simple options?
make clean_all
./configure --enable-int-linalg




Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: Yambo built was fine but it gives error when running

Postby amirmehdi89 » Thu Apr 19, 2018 3:10 pm

Attached please find the requested files.

In any case, you are linking to libraries that finally for some reason are not used.
Can you try to recompile with just this simple options?
make clean_all
./configure --enable-int-linalg


I will do: 1)make clean_all 2) ./configure --enable-int-linalg

But I want to mention two things before doing so:

1. Do you want me to make all after? Or just that and send you the new config.log file?

2. When I compiled it first time, I used so many different options. Do you want me to just use that option?

Thank you.
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Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

Re: Yambo built was fine but it gives error when running

Postby Daniele Varsano » Thu Apr 19, 2018 3:15 pm

Dear Amir,
try to recompile in that simple way and see if it works.
With log I was meaning the standard output, the l_* file if you run in batch, or just redirect the standard output to a file:
> yambo -F input > log

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 2027
Joined: Tue Mar 17, 2009 2:23 pm

Re: Yambo built was fine but it gives error when running

Postby amirmehdi89 » Thu Apr 19, 2018 3:26 pm

The output file. I am about to recompile Yambo again.
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Amir M. Mofrad
University of Missouri-Columbia
Chemical Engineering Department
amirmehdi89
 
Posts: 12
Joined: Wed Apr 04, 2018 12:15 am

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