Petsc doesn't show where in the code the error occurs - linux

Without Petsc, I can see which files, which functions, and which lines an error occurs and is propagated from. With Petsc, I always receive the same error message.
Is there any flag in Petsc that I'm missing?
Thanks.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ./solver on a linux named ion by khoa Sun Apr 10 23:29:33 2011
[0]PETSC ERROR: Libraries linked from /h1/khoa/libs/petsc-3.1/linux/lib
[0]PETSC ERROR: Configure run at Sun Apr 10 17:52:52 2011
[0]PETSC ERROR: Configure options --with-scalar-type=complex --with-clanguage=c++ --with-mpi=1 --with-mpi-dir=/usr/bin
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file

Your code has generated a SEGV, probably by illegally accessing memory. As the error message recommends, you should run using valgrind or gdb, which will allow you to see the stack.

Related

Cannot build YugabyteDB with clang12 in Alma Linux 8.5

[Question posted by a user on YugabyteDB Community Slack]
Debug build does not seem to be working in the clang12 based build:
./yb_build.sh debug --sj
[100%] Linking CXX executable ../../../tests-integration-tests/cdc_service-int-test
[100%] Built target cdc_service-int-test
make: *** [Makefile:101: all] Error 2
real 0m28.279s
user 4m4.235s
sys 0m25.477s
[2022-02-26T15:52:32 yb_build.sh:466 run_cxx_build] C++ build finished with exit code 2 (build type: debug, compiler: clang12). Timing information is available above.
==========================================================================================
YUGABYTE BUILD SUMMARY
==========================================================================================
Build type : debug
C/C++ compiler : clang12
Build architecture : x86_64
Build directory : /yb-source/build/debug-clang12-dynamic
Third-party dir : /opt/yb-build/thirdparty/yugabyte-db-thirdparty-v20211222064150-dd4872fe56-almalinux8-x86_64-clang12
C++ compilation time : 28 seconds
Exit code : 2
------------------------------------------------------------------------------------------
doing
./yb_build.sh debug --clang12 --sj
also results in an error
...
[m-1] In YugabyteDB, setting LC_COLLATE to C and all other locale settings to en_US.UTF-8 by default. Locale support will be enhanced as part of addressing https://github.com/yugabyte/yugabyte-db/issues/1557
[m-1] initdb: invalid locale name "en_US.UTF-8"
[m-1] I0226 15:54:20.630203 15811 pg_wrapper.cc:521] initdb took 124 ms
[m-1] E0226 15:54:20.630272 15811 pg_wrapper.cc:525] initdb failed: Runtime error (yb/yql/pgwrapper/pg_wrapper.cc:467): /yb-source/build/debug-clang12-dynamic/postgres/bin/initdb failed with exit code 1
[m-1] E0226 15:54:20.630429 15811 catalog_manager.cc:7776] initdb failed: Runtime error (yb/yql/pgwrapper/pg_wrapper.cc:467): /yb-source/build/debug-clang12-dynamic/postgres/bin/initdb failed with exit code 1
E0226 15:54:21.075644 15749 external_mini_cluster.cc:1247] master reported an initdb error: Runtime error (yb/yql/pgwrapper/pg_wrapper.cc:467): /yb-source/build/debug-clang12-dynamic/postgres/bin/initdb failed with exit code 1
/yb-source/src/yb/yql/pgwrapper/pg_wrapper_test_base.cc:58: Failure
Failed
Bad status: Runtime error (yb/integration-tests/external_mini_cluster.cc:1248): Failed to start masters.: initdb failed: Runtime error (yb/yql/pgwrapper/pg_wrapper.cc:467): /yb-source/build/debug-clang12-dynamic/postgres/bin/initdb failed with exit code 1
[m-1] W0226 15:54:21.096375 15815 catalog_manager.cc:2084] Tablespace refresh task failed with error Internal error (yb/master/catalog_manager.cc:1929): pg_tablespace table info not found
Test failure stack trace:
/yb-source/src/yb/yql/pgwrapper/pg_wrapper_test_base.cc:58: # 0x7f2962b044e9 yb::pgwrapper::PgWrapperTestBase::SetUp()
/yb-source/src/yb/yql/pgwrapper/create_initial_sys_catalog_snapshot.cc:29: # 0x404d94 yb::pgwrapper::CreateInitialSysCatalogSnapshotTest::SetUp()
I0226 15:54:21.706461 15749 external_mini_cluster.cc:2206] { daemon_id: m-1 bound_rpc: :0 } Starting Shutdown()
I0226 15:54:21.706606 15749 external_mini_cluster.cc:2249] Killing /yb-source/build/debug-clang12-dynamic/tests-pgwrapper/../bin/yb-master with pid 15756 with SIGKILL
I0226 15:54:21.719123 15749 test_util.cc:94] -----------------------------------------------
I0226 15:54:21.719149 15749 test_util.cc:95] Had fatal failures, leaving test files at /tmp/yb_test.tmp.32433.7631.5669.pid15685/create_initial_sys_catalog_snapshot.CreateInitialSysCatalogSnapshotTest.CreateInitialSysCatalogSnapshot.1645890856672495-15749
[ FAILED ] CreateInitialSysCatalogSnapshotTest.CreateInitialSysCatalogSnapshot (5016 ms)
[----------] 1 test from CreateInitialSysCatalogSnapshotTest (5016 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test case ran. (5016 ms total)
[ PASSED ] 0 tests.
[ FAILED ] 1 test, listed below:
[ FAILED ] CreateInitialSysCatalogSnapshotTest.CreateInitialSysCatalogSnapshot
1 FAILED TEST
I0226 15:54:21.751582 15748 run-with-timeout.cc:198] subprocess.Wait finished, waitpid() returned 256
...
[postprocess_test_result.py:246] 2022-02-26 15:54:22,577 INFO: Wrote JSON test report file: /yb-source/build/debug-clang12-dynamic/yb-test-logs/tests-pgwrapper__create_initial_sys_catalog_snapshot/CreateInitialSysCatalogSnapshotTest_CreateInitialSysCatalogSnapshot_test_report.json
(end of standard error)
Traceback (most recent call last):
File "/yb-source/python/yb/gen_initial_sys_catalog_snapshot.py", line 83, in <module>
main()
File "/yb-source/python/yb/gen_initial_sys_catalog_snapshot.py", line 74, in main
raise RuntimeError("initdb failed in %.1f sec" % elapsed_time_sec)
RuntimeError: initdb failed in 6.4 sec
make[2]: *** [src/yb/yql/pgwrapper/CMakeFiles/initial_sys_catalog_snapshot.dir/build.make:70: src/yb/yql/pgwrapper/CMakeFiles/initial_sys_catalog_snapshot] Error 1
make[1]: *** [CMakeFiles/Makefile2:51929: src/yb/yql/pgwrapper/CMakeFiles/initial_sys_catalog_snapshot.dir/all] Error 2
make: *** [Makefile:101: all] Error 2
This happens in Alma Linux 8.5. Any hints?
You need some additional packages and it should work:
dnf install langpacks-en glibc-all-langpacks -y

Check Sum Errors on Checkout

On a virtual host server, I have 1 repository that I can no longer checkout from a remote computer. Checkout works fine if I'm checking out on the server itself. All other repositories on the same virtual host server work without a problem, though none of them have as many files as this one.
When I check out on a remote computer, checkout goes a certain number of files, then starts displaying checksum errors, usually between 2 and 6 at a time. If I delete the checked out folder and try again with a new folder, it will stop after about the same number of files, and the collection of files with checksum errors is different from the previous checkout. Checking out on a different remote computer gets the same random results.
First try:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\settle.shtml':
Error:
Error: expected: b450dbef2a3ceb9542a4e22b4b3e50fe
Error: actual: 9454a4eb5afdbc215bffcc619f537fa3
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndnjv1.shtml':
Error:
Error: expected: e187d974743d0129a6c72413f205458c
Error: actual: 73c0b6aba9a9a42409e2cf7e6d043049
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndfraser.shtml':
Error:
Error: expected: 151444dc294357ba42a640333c94b6f7
Error: actual: 900ffa360acd460773acbe1759578533
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndretn1.shtml':
Error:
Error: expected: 6b8791dc78b0af936d6d7e70e11b69ee
Error: actual: dd7af732663345c6401861c89331adea
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndrfa2.shtml':
Error:
Error: expected: 7451fedd09e1f99adf4c4af2668c4942
Error: actual: 548f947ce54c697957daa4efa4192786
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndpwar3.shtml':
Error:
Error: expected: f7fba4f2a3a468df6c4948eaa034e119
Error: actual: 0f3c2da13e55a7c0271743e7d145cfca
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndrhe1.shtml':
Error:
Error: expected: 32cc673b06be5806bc6bc66000d5ec75
Error: actual: 5356175235c395577793e9fa9f0b9bb7
Second try:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\Petition_Teder_M_1795.shtml':
Error:
Error: expected: c29978209a203cd254c641bd931739e5
Error: actual: e4042c36b5ff42a01eb890044d64b131
Error: Additional errors:
Error: Checksum mismatch for
Error: 'C:\Users\jkorc\Documents\Projects\VHost\RoyalProvincial\Genealogy\Settle\lndbrng1.shtml':
Error:
Error: expected: 6daeec06c6290557ca6b0de0d551fc43
Error: actual: 598d6bad86117e4cf8f384ed523800aa
I created a new repository of the same files on the same server. Same problem, except I start getting checksum errors after downloading only about a dozen files instead of a few hundred. The server is on Subversion 1.13.0, Tortoise is 1.13.1.
Any ideas what kind of problem I should be looking for?
My assumption would be that a certain folder has a corrupt checksum (for whatever reason).
Fist of all I'd check integrity of the SVN. Some instyructions can be found here:
https://www.darklaunch.com/fix-svnadmin-checksum-mismatch-while-reading-representation.html
There's quite some people experiencing this issue. The easy work around normally mentioned is to recreate the repo:
Copy the content to a temporary directory
Add the folder as new one to SVN
As the new content will get new checksums, those should be ok for all folders afterwards
If you want to do some direct editing, here's a post that corrected the SVN files successfully (use at own risk, make backups!)
https://maymay.net/blog/2008/06/17/fix-subversion-checksum-mismatch-error-by-editing-svnentries-file/
I once had strange behaviour when content on net packages had been capped as well. That was caused by the MTU (Maximum Transfer Unit). SVN seem to struggle here as well, so adjust the setting in your network infrastructure. Here's a link to a similar issue with SVN involved.
https://serverfault.com/questions/392881/tortoise-svn-repo-browser-checkout-over-vpn
As summary: To isolate the issue I would do the following steps:
A) See if the repo's SVN metadata is cause:
log to server
copy the repo as filesystem (without SVN data)
create a new repo with the files
connect svn client from other host. If all goes well the SVN metadata is corrupt
b) Check if it's host/network specific
Do the same as A but from other host (= create the repo from there)
List item
c) Check if network MTU is ok
do check up to which size packets will be transferred ok (will not go into details as this is very OS/infrastructure related, but you'll find lot's of infos)
note hops/VPNs/multiple routers/IPv4-IPv6 can all play into this
Having written all that: Did you crosscheck behaviour with a second SVN client in the first place? Might be the first thing to do.

Error while compiling opentsDB for Cassandra using AsyncCassandra

I am following below link to build AsyncCassandra -
https://github.com/OpenTSDB/asynccassandra
But I am getting following error :
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /root/asynccassandra/src/org/hbase/async/HBaseClient.java:[304,34] error: cannot find symbol
[ERROR] symbol: variable ConsistencyLevel
location: class HBaseClient
/root/asynccassandra/src/org/hbase/async/HBaseClient.java:[303,25] [deprecation] BoundedExponentialBackoff(long,int,int) in BoundedExponentialBackoff has been deprecated
[ERROR] /root/asynccassandra/src/org/hbase/async/HBaseClient.java:[311,35] error: cannot find symbol
It looks like source code is missing
import com.netflix.astyanax.model.ConsistencyLevel;
But in reality, the astynax project that is used for it is already retired, and shouldn't be used.

Cross Compiling on OSX to Raspberry Pi

I am trying to configure an environment on my osx machine that will allow me to cross compile arm6 applications for the Raspberry Pi. I seem to be runnning into a wall when it comes to setting up the toolchain. I am using crosstool-ng and am following multiple guides on setup but my issue comes down to when running the ct-ng build command.
Once I run this command everything seems to be running fine until I get to trying to build the binutils. Once it reaches this depenency it will eventually fail no mater what I do.
This is the ouput that I am seeing:
[INFO ] Installing binutils for host
[EXTRA] Configuring binutils
[EXTRA] Building binutils
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:51:72: error: use of undeclared identifier 'do_not_use_isalnum_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:59:72: error: use of undeclared identifier 'do_not_use_isalpha_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:75:72: error: use of undeclared identifier 'do_not_use_iscntrl_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:83:72: error: use of undeclared identifier 'do_not_use_isdigit_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:91:72: error: use of undeclared identifier 'do_not_use_isgraph_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:99:72: error: use of undeclared identifier 'do_not_use_islower_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:107:72: error: use of undeclared identifier 'do_not_use_isprint_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:115:72: error: use of undeclared identifier 'do_not_use_ispunct_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:123:72: error: use of undeclared identifier 'do_not_use_isspace_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:131:72: error: use of undeclared identifier 'do_not_use_isupper_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:139:73: error: use of undeclared identifier 'do_not_use_isxdigit_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:147:72: error: use of undeclared identifier 'do_not_use_tolower_with_safe_ctype'
[ERROR] /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cctype:155:72: error: use of undeclared identifier 'do_not_use_toupper_with_safe_ctype'
[ERROR] make[5]: *** [binary.o] Error 1
[ERROR] make[4]: *** [all-recursive] Error 1
[ERROR] make[3]: *** [all] Error 2
[ERROR] make[2]: *** [all-gold] Error 2
[ERROR] make[1]: *** [all] Error 2
[ERROR]
[ERROR] >>
[ERROR] >> Build failed in step 'Installing binutils for host'
[ERROR] >> called in step '(top-level)'
[ERROR] >>
[ERROR] >> Error happened in: CT_DoExecLog[scripts/functions#216]
[ERROR] >> called from: do_binutils_backend[scripts/build/binutils/binutils.sh#236]
[ERROR] >> called from: do_binutils_for_host[scripts/build/binutils/binutils.sh#101]
[ERROR] >> called from: main[scripts/crosstool-NG.sh#638]
[ERROR] >>
[ERROR] >> For more info on this error, look at the file: 'build.log'
[ERROR] >> There is a list of known issues, some with workarounds, in:
[ERROR] >> '/usr/local/Cellar/crosstool-ng/1.21.0/share/doc/crosstool-ng/ct-ng.1.21.0/B - Known issues.txt'
[ERROR]
[ERROR] (elapsed: 5:11.00)
[05:12] / make: *** [build] Error 1
If anyone has ran into this issue and knows how to fix it. It would be much appreciated. Trying to build from source on the Pi (Model A+ has proven pretty tough as it will eventually crash)
Thank you.
Gold linker cannot be compiled on Clang 6-7 for now. You should be able to proceed if the linker is disabled via ct-ng menuconfig in Binary Utilities - Linkers to enable.

Fatal error: require_once(): Failed opening required 'pre.php' in /usr/share/tuleap/src/www/index.php

I have installed xampp and then tuleap in centos and gave /usr/share/tuleap/src/www as document root in /etc/httpd/conf/httpd.conf
When I hit the url, I am getting the following error:
Warning: require_once(pre.php): failed to open stream: No such file or directory in /usr/share/tuleap/src/www/index.php on line 9
Fatal error: require_once(): Failed opening required 'pre.php' (include_path='.:/opt/lampp/lib/php') in /usr/share/tuleap/src/www/index.php on line 9
I am also seeing that the document root points to /usr/share/tuleap/src/www and pre.php is not in this folder. Instead it is at include/pre.php I am totally confused on this directory structure. I didn't change any code after installing tuleap.
Please let me know how to fix this issue.
Thanks in advance!

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