{2023.06}[2023a] acpype v2023.10.27 #1332
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bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2 |
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AmberTools 23.6 is picking up the wrong Python: |
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casparvl
reviewed
Jan 27, 2026
easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml
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bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2 |
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casparvl
reviewed
Jan 27, 2026
easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml
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…23a.yml Co-authored-by: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
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bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen2 |
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bot: build repo:eessi.io-2023.06-software instance:eessi-bot-mc-aws for:arch=x86_64/amd/zen3 |
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Collaborator
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This build seems to hang on all ARM architectures. In a 1381 minutes of CPU time, that's almost the full 23:23h this job has now been running. |
Collaborator
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This is almost certainly the test step, I also see a process: |
Collaborator
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Ran a few |
Collaborator
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Also, for 125692, I downright killed easybuild. I hope I can still get access to the temporary log file... |
Collaborator
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Hm... log file just says: Nothing more. Not very useful. |
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bot:cancel 125690,125691 |
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bot:cancel 14401394 |
Contributor
Author
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I remember |
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bot:cancel jobid:14401394 |
Collaborator
Yeah, I'm pretty sure this is a real hang. I think the best way to investigate is a build with |
Contributor
Author
I guess i can get an interactive shell on the AWS build cluster as i did for the QE benchmarks and test from there |
Contributor
Author
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Curios if it could be something similar to http://archive.ambermd.org/201606/0163.html (@boegel ) |
Contributor
Author
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Man this was a rabbithole, the hang boils down to https://bugs.webkit.org/show_bug.cgi?id=144439 which causes an infinite loops in int DetectBinaryFile(char* fname)
{
int isbinary;
long long int il, fsize;
char testchar;
FILE *finp;
// Detect binary files as those having any byte whose value is outside the
// range [0, 127].
if ((finp = fopen(fname, "r")) == NULL) {
printf("DetectBinaryFile >> Error. File %s does not exist.\n", fname);
exit(1);
}
isbinary = 0;
while ((testchar = fgetc(finp)) != EOF && isbinary == 0) {
if (testchar < 0) {
isbinary = 1;
break;
}
}
fclose(finp);
return isbinary;
}Also very easy to reproduce with a Test prpgram
#include <stdio.h>
#include <stdlib.h>
int DetectBinaryFile(char* fname)
{
int isbinary;
long long int il, fsize;
char testchar;
FILE *finp;
// Detect binary files as those having any byte whose value is outside the
// range [0, 127].
if ((finp = fopen(fname, "r")) == NULL) {
printf("DetectBinaryFile >> Error. File %s does not exist.\n", fname);
exit(1);
}
isbinary = 0;
int cnt = 0;
while ((testchar = fgetc(finp)) != EOF && isbinary == 0) {
printf("%c %d\n", testchar, testchar);
if (testchar < 0) {
isbinary = 1;
printf("BINARY!!!!: BREAK!\n");
break;
}
cnt++;
if (cnt > 10000000) {
printf("More than 10 milion chars... EXIT\n");
printf("EOF %%d: %d %%x: %x\n", EOF, EOF);
break;
}
}
fclose(finp);
return isbinary;
}
int main(int argc, char *argv[])
{
char* filename = argv[1];
int result = DetectBinaryFile(filename);
if (result) {
printf("The file %s is a binary file.\n", filename);
} else {
printf("The file %s is a text file.\n", filename);
}
return 0;
}replacing the char with an |
Contributor
Author
|
Apparently this was fixed at some point. In AmberTools 25 they have //-----------------------------------------------------------------------------
// DetectBinaryFile: runs a simple test to verify whether a file is ascii text
// or instead can only be parsed as a binary file. Returns
// 0 for ascii, 1 for binary.
//
// Arguments:
// fname: the name of the file
//-----------------------------------------------------------------------------
int DetectBinaryFile(char* fname)
{
int isbinary;
long long int il, fsize;
int testchar;
FILE *finp;
// Detect binary files as those having any byte whose value is outside the
// range [0, 127].
if ((finp = fopen(fname, "r")) == NULL) {
printf("DetectBinaryFile >> Error. File %s does not exist.\n", fname);
exit(1);
}
isbinary = 0;
while ((testchar = fgetc(finp)) != EOF && isbinary == 0) {
if (testchar < 0) {
isbinary = 1;
break;
}
}
fclose(finp);
return isbinary;
}Not sure if testing for |
Contributor
Author
|
@casparvl Was able to run an |
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