xPerm : unable to connect to the external executable
Nux
First, as information, I'm working on Mathematica 13.0 on a Fedora 37 distrib.
I've installed xAct following the installation notes (tried the system wide and single user one, before posting here). However it seems impossible to import xPerm : it gets stuck on the "Connecting to external linux executable...".
Moreover, I can import xTensor, xCore, xCoba without any issues to connect to the external executable. (Still, since xTensor import xPerm, I need to execute << xAct`xTensor`;, abort, and then execute it again, probably because it updates the ContextPath and then skip the import of xPerm.)
I've also tried to recompile xPerm using mprep and mcc, but still the same issue in the end.
I'd like to add that however :
$xpermLink =Install["path/to/xperm.linux"]
return a LinkObject without any issues. But in the end, since stuff like $xpermQ and such are undefined, it does not work when working on real stuff.
Is there any idea on what to do at this point ?
Thank you !
Ilham Prasetyo
Thomas Bäckdahl
xAct really needs a new release. Mathematica changes the versions of the mathlink communication protocol from time to time. There are also name conflicts with the newest version of Mathematica.
In the meantime. What have you tried?
If you have not tried it already, try
cd ~/.Wolfram/Applications/xAct/xPerm/mathlink
mcc xperm.tm -O3 -o xperm.linux.64-bit
This should recompile the external mathlink file to fit your system.
Regards
Thomas
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Ilham Prasetyo
Package xAct`xCore` version 0.6.10, {2018,2,28}
CopyRight (C) 2007-2020, Jose M. Martin-Garcia, under the General Public License.
------------------------------------------------------------
This package comes with ABSOLUTELY NO WARRANTY; for details type Disclaimer[]. This is free software, and you are welcome to redistribute it under certain conditions. See the General Public License for details.
------------------------------------------------------------
------------------------------------------------------------
Package xAct`xPerm` version 1.2.3, {2015,8,23}
CopyRight (C) 2003-2020, Jose M. Martin-Garcia, under the General Public License.
Connecting to external linux executable...
xperm.linux.64-bit.tm.c: xperm.tm: In function ‘main’:
xperm.tm:573:5: warning: old-style function definition [-Wold-style-definition]
573 | int main(argc, argv)
| ^~~~
In file included from xperm.tm:24:
In function ‘copy_list’,
inlined from ‘copy_list’ at xperm.c:283:6,
inlined from ‘sort’ at xperm.c:389:2,
inlined from ‘double_coset_rep’ at xperm.c:1973:2:
xperm.c:285:9: warning: ‘__builtin_memcpy’ writing between 18446744065119617024 and 18446744073709551612 bytes into a region of size between 0 and 9223372036854775807 [-Wstringop-overflow=]
285 | memmove(list2, list1, n*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xperm.c: In function ‘double_coset_rep’:
xperm.c:1738:35: note: destination object of size [0, 9223372036854775807] allocated by ‘malloc’
1738 | int *drummytmp2= (int*)malloc( n*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~
In function ‘copy_list’,
inlined from ‘copy_list’ at xperm.c:283:6,
inlined from ‘sort’ at xperm.c:389:2,
inlined from ‘double_coset_rep’ at xperm.c:1973:2:
xperm.c:285:9: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
285 | memmove(list2, list1, n*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/ld: cannot find -luuid: No such file or directory
collect2: error: ld returned 1 exit status
Thomas Bäckdahl
Hi!
Yes, Mathematica actually changed name to Wolfram fairly recently, so if you are using a slightly older version you should use .Mathematica instead of .Wolfram
From the error messages it looks like you might be missing the
uuid libraries.
I have not tried this recently, but a while ago I had the same
problem on a Raspberry Pi. Then the following helped
sudo apt-get install uuid-dev
mcc xperm.tm -luuid -O3 -o xperm.linux.64-bit
Still you need to do this in the mathlink folder.
I hope this helps.
Regards
Thomas
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Ilham Prasetyo
Block[{Print}, << xAct`xPert`]
Block[{Print}, << xAct`xCoba`]
Block[{Print}, << xAct`xTras`]
Block[{Print}, << xAct`TexAct`]
$PrePrint = ScreenDollarIndices;
$CovDFormat = "Prefix";
$DefInfoQ = False;
$CVVerbose = False;
Thomas Bäckdahl
xPerm has Mathematica code that can do the same thing as the external executable. If the link to the external executable fails, the much slower internal code will be used instead.
Your system is not too new, but your Mathematica version is fairly old. The current version is 14.3.
Unfortunately, one can not send executable files via google groups, so I can not easily send my latest compiled version of xPerm for linux.
The only error message you listed from the compiler was "cannot find -luuid". Did installing installing uuid-dev fix that problem?
The message from Mathematica: "LinkOpen::linke: Could not find MathLink executable" indicates that it can not find the file, not that the file is incompatible with your system.
After loading xPerm, check the $xActDirectory variable. In your case I expect it to be "/home/yourusername/.Mathematica/Applications/xAct/"
Make sure that xperm.linux.64-bit is in the xPerm/mathlink sub-folder and has the permissions "Allow executing file as program".
Regards
Thomas
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Ilham Prasetyo
Dear Thomas,
Now it works! Thank you so much for your help!
It turns out that perhaps either I forgot to allow xperm.linux.64-bit to be executed as a program, or I used a different mcc, or something else. The details are shown below.
----------------------------
> The only error message you listed from the compiler was "cannot find -luuid". Did installing installing uuid-dev fix that problem?
Somehow it still persists.
> After loading xPerm, check the $xActDirectory variable. In your case I expect it to be "/home/yourusername/.Mathematica/Applications/xAct/"
Yes, it is.
> Make sure that xperm.linux.64-bit is in the xPerm/mathlink sub-folder and has the permissions "Allow executing file as program".
I checked it and it somehow vanished. Then I just copy whole xAct folder into ~./Mathematica/Applications/. Then I made sure xperm.linux.64-bit , xperm.linux.32-bit, xperm.linux.pre6, xperm.win64 and xperm.win32 are all allowed to be executed as program. Then I did the mcc step again but the problem persists, both using:
$ mcc xperm.tm -luuid -O3 -o xperm.linux.64-bit
$ /usr/local/Wolfram/Mathematica/12.0/Executables/mcc xperm.tm -luuid -O3 -o xperm.linux.64-bit
Surprisingly, when I checked it inside Mathematica by calling xPerm, now the error with Mathlink is gone!
Package xAct`xPerm` version 1.2.3, {2015,8,23}
CopyRight (C) 2003-2020, Jose M. Martin-Garcia, under the General Public License.
Connecting to external linux executable...
Connection established.
-----------------------
Best regards,Ilham