Error in /usr/local/dalton/dalton.x, exit code 127

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saisudhakar
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Error in /usr/local/dalton/dalton.x, exit code 127

Post by saisudhakar » 23 Nov 2015, 05:23

Hi, I am trying to do TPA calculation but it did not generate .out file and terminated with exit code127.

The following error observed in the process

/usr/local/dalton/dalton.x: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
Error in /usr/local/dalton/dalton.x, exit code 127
tar: Cowardly refusing to create an empty archive
Try `tar --help' or `tar --usage' for more information.
pehf_2pa.tar.gz has been copied to /root/Desktop/A/pehf_2pa
DALTON.OUT has not been created from the present run.
/scratch/DALTON_scratch_root/pehf_2pa_12881 is therefore not deleted by this script.
List of created files in /scratch/DALTON_scratch_root/pehf_2pa_12881 :
total 20
8 -rw------- 1 root root 5827 Nov 23 09:38 POTENTIAL.INP
4 -rw-r--r-- 1 root root 20 Nov 23 09:38 pehf_2pa.tar.gz
4 -rw------- 1 root root 520 Nov 23 09:38 MOLECULE.INP
4 -rw------- 1 root root 110 Nov 23 09:38 DALTON.INP


Please tell me where it went wrong.

taylor
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Re: Error in /usr/local/dalton/dalton.x, exit code 127

Post by taylor » 24 Nov 2015, 17:34

I think expecting anyone to tell you "where it went wrong" is difficult when we have no idea what "it" is (other than it's a TPA calculation of some sort). If you have no output file at all, just an error file, it would be useful to post the input file(s). If there is an output file, then simply post that: it should contain the input and output files. How are you invoking the program, by using the Dalton runscript (just named dalton)? What queueing system, if any?

Let me make a separate point. The program seems to want to write files (e.g., output) into /root/Desktop/<something-or-other>. This would only be possible if you are either running as the root user, or you have changed the permissions on the root user's home directory/subdirectory to allow any user to write into them. Either of these alternatives is a very bad idea. A task that runs as root has immense privileges, and you are running a program that you have simply downloaded and built, so you have no real idea what damage could occur. For example, suppose for whatever reason the runscript or the program itself were to assign / as the program's scratch directory (using an environment variable SCRATCHDIR, say) at runtime. Since the clean-up at the end of the Dalton script basically does

Code: Select all

rm -rf $SCRATCHDIR
you will see that this is equivalent to

Code: Select all

rm -rf /
which is almost certainly not what you want to do! (And don't believe the old chestnut that this will only delete files until it tries to remove "rm" itself...) Similarly, changing permissions on root's directory hierarchy is not recommended either --- it would let someone write malicious code for root/others to run, for example.

Best regards
Pete

taylor
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First name(s): Peter
Middle name(s): Robert
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Affiliation: Tianjin University
Country: China

Re: Error in /usr/local/dalton/dalton.x, exit code 127

Post by taylor » 24 Nov 2015, 17:41

Perhaps by "it" you meant the topmost message, which is a failure to load the libquadmath shared library? This is the quadruple-precision maths library supplied with gcc (from version 4.6 on). Did you compile Dalton yourself? If so, which compilers? Are you running on the machine you compiled on? I cannot understand why quad-precision maths is needed for a Dalton build, and if it is simply a compiler default to include it for linking, then I would expect the compiler suite to include this library. But if you compile with one version and then run on a different machine, it is important to ensure the software stacks are consistent on the two machines.

Best regards
Pete

taylor
Posts: 545
Joined: 15 Oct 2013, 05:37
First name(s): Peter
Middle name(s): Robert
Last name(s): Taylor
Affiliation: Tianjin University
Country: China

Re: Error in /usr/local/dalton/dalton.x, exit code 127

Post by taylor » 24 Nov 2015, 17:48

You might look at
http://glennklockwood.blogspot.no/2014/ ... trans.html
which suggests some default features of gcc have changed. If indeed the problem is that your build is trying to "promote" double precision variables to quad precision, it is imperative you disable this. Running in quad precision will lose you close to an order of magnitude in performance, and even worse for some operations. I cannot say much more because I do not build with gfortran/gcc.

Best regards
Pete

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