Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Ubuntu VM on Apple Silicon fails to load or compile devIocStats #183

Open
prichards-wmko opened this issue Jan 29, 2025 · 3 comments
Open

Ubuntu VM on Apple Silicon fails to load or compile devIocStats #183

prichards-wmko opened this issue Jan 29, 2025 · 3 comments

Comments

@prichards-wmko
Copy link

I have softIOC code developed on other systems that is failing to run on my Apple Silicon Macbook Pro M2 (in a Parallels virtual machine running Ubuntu), and it appears to be due to the devIocStats feature causing a buffer overflow and then core dump.

My machine:

Linux vm-ubuntu24 6.8.0-51-generic #52-Ubuntu SMP PREEMPT_DYNAMIC Thu Dec  5 13:32:09 UTC 2024 aarch64 aarch64 aarch64 GNU/Linux

The easiest way to demonstrate the error; this is on a machine installed last July. I wasn't running devIocStats on it until now.

Python 3.12.4 | packaged by Anaconda, Inc. | (main, Jun 18 2024, 15:03:55) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from softioc import softioc
INFO: PVXS QSRV2 is loaded, permitted, and ENABLED.
>>> softioc.devIocStats('test')
*** buffer overflow detected ***: terminated
Aborted (core dumped)

I also tried to reproduce the problem on a freshly installed Ubuntu 24.04 machine I just made for a test. It fails to compile.

Collecting softioc
  Downloading softioc-4.5.0.tar.gz (82 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting epicscorelibs<7.0.7.99.2,>=7.0.7.99.1.1 (from softioc)
  Using cached epicscorelibs-7.0.7.99.1.1-cp312-cp312-linux_aarch64.whl
Collecting pvxslibs>=1.2.2 (from softioc)
  Downloading pvxslibs-1.3.2.tar.gz (660 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 660.7/660.7 kB 411.8 kB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /usr/local/Anaconda3-2024.10-1/lib/python3.12/site-packages (from softioc) (1.26.4)
Collecting epicsdbbuilder>=1.4 (from softioc)
  Downloading epicsdbbuilder-1.5-py3-none-any.whl.metadata (2.8 kB)
Requirement already satisfied: setuptools in /usr/local/Anaconda3-2024.10-1/lib/python3.12/site-packages (from epicscorelibs<7.0.7.99.2,>=7.0.7.99.1.1->softioc) (75.1.0)
Collecting setuptools-dso>=2.11a2 (from epicscorelibs<7.0.7.99.2,>=7.0.7.99.1.1->softioc)
  Using cached setuptools_dso-2.11-py2.py3-none-any.whl.metadata (1.6 kB)
Downloading epicsdbbuilder-1.5-py3-none-any.whl (23 kB)
Using cached setuptools_dso-2.11-py2.py3-none-any.whl (23 kB)
Building wheels for collected packages: softioc, pvxslibs
  Building wheel for softioc (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for softioc (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [149 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/__init__.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/__main__.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/_version_git.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/alarm.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/asyncio_dispatcher.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/builder.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/cothread_dispatcher.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/device.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/device_core.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/fields.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/imports.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/pvlog.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/pythonSoftIoc.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/softioc.py -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/access.acf -> build/lib.linux-aarch64-cpython-312/softioc
      copying softioc/device.dbd -> build/lib.linux-aarch64-cpython-312/softioc
      creating build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/Makefile -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStats.dbd -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStats.h -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStatsAnalog.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStatsString.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStatsSub.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStatsTest.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devIocStatsWaveform.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      copying softioc/iocStats/devIocStats/devVxStats.dbd -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      creating build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/Makefile -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/access.db -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/access.doc -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/ioc.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocAdminRTEMS.substitutions -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocAdminScanMon.substitutions -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocAdminSoft.substitutions -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocAdminVxWorks.substitutions -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocCluster.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocEnvVar.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocGeneralTime.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocQueue.db -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocRTEMSOnly.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocRTOS.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocScanMon.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocScanMonSum.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      copying softioc/iocStats/iocAdmin/Db/iocVxWorksOnly.template -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/iocAdmin/Db
      creating build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/devIocStatsOSD.h -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdBootInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdClustInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdCpuUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdCpuUtilization.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdFdUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdHostInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdIFErrors.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdMemUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdPIDInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdPwdInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdSuspTasks.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdSystemInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      copying softioc/iocStats/devIocStats/os/default/osdWorkspaceUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      creating build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Darwin
      copying softioc/iocStats/devIocStats/os/Darwin/devIocStatsOSD.h -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Darwin
      creating build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/devIocStatsOSD.h -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/osdBootInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/osdCpuUtilization.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/osdFdUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/osdHostInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/osdMemUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      copying softioc/iocStats/devIocStats/os/WIN32/osdSystemInfo.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/WIN32
      creating build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Linux
      copying softioc/iocStats/devIocStats/os/Linux/osdCpuUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Linux
      copying softioc/iocStats/devIocStats/os/Linux/osdCpuUtilization.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Linux
      copying softioc/iocStats/devIocStats/os/Linux/osdFdUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Linux
      copying softioc/iocStats/devIocStats/os/Linux/osdMemUsage.c -> build/lib.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Linux
      running build_ext
      building 'softioc._extension' extension
      creating build/temp.linux-aarch64-cpython-312/softioc
      creating build/temp.linux-aarch64-cpython-312/softioc/iocStats/devIocStats
      creating build/temp.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/Linux
      creating build/temp.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/os/default
      gcc -pthread -B /usr/local/Anaconda3-2024.10-1/compiler_compat -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -Wall -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -D_GNU_SOURCE -D_DEFAULT_SOURCE -Dlinux -DUNIX -D_GLIBCXX_USE_CXX11_ABI=1 -I/tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include -Isoftioc/iocStats/devIocStats -Isoftioc/iocStats/devIocStats/os/Linux -Isoftioc/iocStats/devIocStats/os/default -I/usr/local/Anaconda3-2024.10-1/include/python3.12 -c softioc/extension.c -o build/temp.linux-aarch64-cpython-312/softioc/extension.o -g0 -std=c99
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccess.h:20,
                       from softioc/extension.c:7:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbBase.h:164:5: warning: ‘rset’ is deprecated [-Wdeprecated-declarations]
        164 |     rset            *prset;
            |     ^~~~
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbBase.h:22:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/recSup.h:68:8: note: declared here
         68 | struct rset {   /* record support entry table */
            |        ^~~~
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccess.h:24:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccessDefs.h:210:42: warning: ‘rset’ is deprecated [-Wdeprecated-declarations]
        210 | DBCORE_API rset * dbGetRset(const struct dbAddr *paddr);
            |                                          ^~~~~~
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/recSup.h:68:8: note: declared here
         68 | struct rset {   /* record support entry table */
            |        ^~~~
      gcc -pthread -B /usr/local/Anaconda3-2024.10-1/compiler_compat -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -Wall -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -D_GNU_SOURCE -D_DEFAULT_SOURCE -Dlinux -DUNIX -D_GLIBCXX_USE_CXX11_ABI=1 -I/tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include -Isoftioc/iocStats/devIocStats -Isoftioc/iocStats/devIocStats/os/Linux -Isoftioc/iocStats/devIocStats/os/default -I/usr/local/Anaconda3-2024.10-1/include/python3.12 -c softioc/iocStats/devIocStats/devIocStatsAnalog.c -o build/temp.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/devIocStatsAnalog.o -g0 -std=c99
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccess.h:20,
                       from softioc/iocStats/devIocStats/devIocStatsAnalog.c:118:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbBase.h:164:5: warning: ‘rset’ is deprecated [-Wdeprecated-declarations]
        164 |     rset            *prset;
            |     ^~~~
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbBase.h:22:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/recSup.h:68:8: note: declared here
         68 | struct rset {   /* record support entry table */
            |        ^~~~
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccess.h:24:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccessDefs.h:210:42: warning: ‘rset’ is deprecated [-Wdeprecated-declarations]
        210 | DBCORE_API rset * dbGetRset(const struct dbAddr *paddr);
            |                                          ^~~~~~
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/recSup.h:68:8: note: declared here
         68 | struct rset {   /* record support entry table */
            |        ^~~~
      gcc -pthread -B /usr/local/Anaconda3-2024.10-1/compiler_compat -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -Wall -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -D_GNU_SOURCE -D_DEFAULT_SOURCE -Dlinux -DUNIX -D_GLIBCXX_USE_CXX11_ABI=1 -I/tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include -Isoftioc/iocStats/devIocStats -Isoftioc/iocStats/devIocStats/os/Linux -Isoftioc/iocStats/devIocStats/os/default -I/usr/local/Anaconda3-2024.10-1/include/python3.12 -c softioc/iocStats/devIocStats/devIocStatsString.c -o build/temp.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/devIocStatsString.o -g0 -std=c99
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccess.h:20,
                       from softioc/iocStats/devIocStats/devIocStatsString.c:93:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbBase.h:164:5: warning: ‘rset’ is deprecated [-Wdeprecated-declarations]
        164 |     rset            *prset;
            |     ^~~~
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbBase.h:22:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/recSup.h:68:8: note: declared here
         68 | struct rset {   /* record support entry table */
            |        ^~~~
      In file included from /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccess.h:24:
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/dbAccessDefs.h:210:42: warning: ‘rset’ is deprecated [-Wdeprecated-declarations]
        210 | DBCORE_API rset * dbGetRset(const struct dbAddr *paddr);
            |                                          ^~~~~~
      /tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include/recSup.h:68:8: note: declared here
         68 | struct rset {   /* record support entry table */
            |        ^~~~
      gcc -pthread -B /usr/local/Anaconda3-2024.10-1/compiler_compat -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -Wall -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -O3 -isystem /usr/local/Anaconda3-2024.10-1/include -fPIC -D_GNU_SOURCE -D_DEFAULT_SOURCE -Dlinux -DUNIX -D_GLIBCXX_USE_CXX11_ABI=1 -I/tmp/pip-build-env-f4dm2sp3/overlay/lib/python3.12/site-packages/epicscorelibs/include -Isoftioc/iocStats/devIocStats -Isoftioc/iocStats/devIocStats/os/Linux -Isoftioc/iocStats/devIocStats/os/default -I/usr/local/Anaconda3-2024.10-1/include/python3.12 -c softioc/iocStats/devIocStats/devIocStatsSub.c -o build/temp.linux-aarch64-cpython-312/softioc/iocStats/devIocStats/devIocStatsSub.o -g0 -std=c99
      softioc/iocStats/devIocStats/devIocStatsSub.c: In function ‘scanMonInit’:
      softioc/iocStats/devIocStats/devIocStatsSub.c:91:16: error: implicit declaration of function ‘malloc’ [-Wimplicit-function-declaration]
         91 |   psub->dpvt = malloc(sizeof(epicsTimeStamp));
            |                ^~~~~~
      softioc/iocStats/devIocStats/devIocStatsSub.c:26:1: note: include ‘<stdlib.h>’ or provide a declaration of ‘malloc’
         25 | #include "devIocStats.h"
        +++ |+#include <stdlib.h>
         26 |
      softioc/iocStats/devIocStats/devIocStatsSub.c:91:16: warning: incompatible implicit declaration of built-in function ‘malloc’ [-Wbuiltin-declaration-mismatch]
         91 |   psub->dpvt = malloc(sizeof(epicsTimeStamp));
            |                ^~~~~~
      softioc/iocStats/devIocStats/devIocStatsSub.c:91:16: note: include ‘<stdlib.h>’ or provide a declaration of ‘malloc’
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for softioc
  Building wheel for pvxslibs (pyproject.toml) ... done
  Created wheel for pvxslibs: filename=pvxslibs-1.3.2-cp312-cp312-linux_aarch64.whl size=1947218 sha256=4d61814d8b17ea04a967b5889969140bac7584c0299ea5937933f3e18586de4b
  Stored in directory: /root/.cache/pip/wheels/cb/b2/4e/5385924e571775421b6050a485cc1960c26227e972b21026c8
Successfully built pvxslibs
Failed to build softioc
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (softioc)
AlexanderWells-diamond added a commit that referenced this issue Jan 29, 2025
@AlexanderWells-diamond
Update iocStats to latest version
2c7308f 
This may resolve issue #183.
@AlexanderWells-diamond
Copy link
Collaborator

Sorry for the issues you are encountering. We unfortunately have no MacOS machines to test against - and one of our dependencies also does not currently support arm64.

If you are willing to test it, I have a potential solution: could you please try installing pythonSoftIOC directly from a branch using this command:

pip install git+https://github.com/DiamondLightSource/pythonSoftIOC.git@issue_183

Hopefully that will compile and run successfully!

@prichards-wmko
Copy link
Author

This installed as expected but did not fix the underlying issue.

First, the install, if it helps to see it:

# /usr/local/anaconda/bin/pip install git+https://github.com/DiamondLightSource/pythonSoftIOC.git@issue_183
DEPRECATION: Loading egg at /usr/local/anaconda3-2024.06/lib/python3.12/site-packages/Adafruit_BBIO-1.2.0-py3.12-linux-aarch64.egg is deprecated. pip 24.3 will enforce this behaviour change. A possible replacement is to use pip for package installation.. Discussion can be found at https://github.com/pypa/pip/issues/12330
Collecting git+https://github.com/DiamondLightSource/pythonSoftIOC.git@issue_183
  Cloning https://github.com/DiamondLightSource/pythonSoftIOC.git (to revision issue_183) to /tmp/pip-req-build-c4tzm0j3
  Running command git clone --filter=blob:none --quiet https://github.com/DiamondLightSource/pythonSoftIOC.git /tmp/pip-req-build-c4tzm0j3
  Running command git checkout -b issue_183 --track origin/issue_183
  Switched to a new branch 'issue_183'
  branch 'issue_183' set up to track 'origin/issue_183'.
  Resolved https://github.com/DiamondLightSource/pythonSoftIOC.git to commit 2c7308fa4151f7dd0673439e7f0a14f5418bcc35
  Running command git submodule update --init --recursive -q
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting epicscorelibs<7.0.7.99.2,>=7.0.7.99.1.1 (from softioc==4.5.0+53.g2c7308f)
  Using cached epicscorelibs-7.0.7.99.1.1-cp312-cp312-linux_aarch64.whl
Collecting pvxslibs>=1.3.2a2 (from softioc==4.5.0+53.g2c7308f)
  Downloading pvxslibs-1.3.2.tar.gz (660 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 660.7/660.7 kB 2.1 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /usr/local/anaconda3-2024.06/lib/python3.12/site-packages (from softioc==4.5.0+53.g2c7308f) (1.26.4)
Requirement already satisfied: epicsdbbuilder>=1.4 in /usr/local/anaconda3-2024.06/lib/python3.12/site-packages (from softioc==4.5.0+53.g2c7308f) (1.5)
Requirement already satisfied: pyyaml>=6.0 in /usr/local/anaconda3-2024.06/lib/python3.12/site-packages (from softioc==4.5.0+53.g2c7308f) (6.0.1)
Requirement already satisfied: setuptools in /usr/local/anaconda3-2024.06/lib/python3.12/site-packages (from epicscorelibs<7.0.7.99.2,>=7.0.7.99.1.1->softioc==4.5.0+53.g2c7308f) (69.5.1)
Collecting setuptools-dso>=2.11a2 (from epicscorelibs<7.0.7.99.2,>=7.0.7.99.1.1->softioc==4.5.0+53.g2c7308f)
  Using cached setuptools_dso-2.11-py2.py3-none-any.whl.metadata (1.6 kB)
Using cached setuptools_dso-2.11-py2.py3-none-any.whl (23 kB)
Building wheels for collected packages: softioc, pvxslibs
  Building wheel for softioc (pyproject.toml) ... done
  Created wheel for softioc: filename=softioc-4.5.0+53.g2c7308f-cp312-cp312-linux_aarch64.whl size=120127 sha256=1607d0a17d35f3de38f5dd97e1c9f50186c4cd246773d541cdfdbf3a5c29d9d9
  Stored in directory: /tmp/pip-ephem-wheel-cache-d0xd9uz8/wheels/10/16/bd/40b31b942f84a986e5010316fe2c4382fa39cb10998831feaa
  Building wheel for pvxslibs (pyproject.toml) ... done
  Created wheel for pvxslibs: filename=pvxslibs-1.3.2-cp312-cp312-linux_aarch64.whl size=1950003 sha256=6411f1de6d2796090a34678f6d2920afd66859b4b1497402a042bdf4fdc0dd6f
  Stored in directory: /root/.cache/pip/wheels/cb/b2/4e/5385924e571775421b6050a485cc1960c26227e972b21026c8
Successfully built softioc pvxslibs
Installing collected packages: setuptools-dso, epicscorelibs, pvxslibs, softioc
  Attempting uninstall: setuptools-dso
    Found existing installation: setuptools-dso 2.10
    Uninstalling setuptools-dso-2.10:
      Successfully uninstalled setuptools-dso-2.10
  Attempting uninstall: epicscorelibs
    Found existing installation: epicscorelibs 7.0.7.99.0.2
    Uninstalling epicscorelibs-7.0.7.99.0.2:
      Successfully uninstalled epicscorelibs-7.0.7.99.0.2
  Attempting uninstall: pvxslibs
    Found existing installation: pvxslibs 1.3.1
    Uninstalling pvxslibs-1.3.1:
      Successfully uninstalled pvxslibs-1.3.1
  Attempting uninstall: softioc
    Found existing installation: softioc 4.5.0
    Uninstalling softioc-4.5.0:
      Successfully uninstalled softioc-4.5.0
Successfully installed epicscorelibs-7.0.7.99.1.1 pvxslibs-1.3.2 setuptools-dso-2.11 softioc-4.5.0+53.g2c7308f

The epicscorelibs packages it's own libstdc++.so.6 version for some reason. This does not match the one in my Ubuntu release and it causes the module to fail to load:

$ /usr/local/anaconda/bin/python3
Python 3.12.4 | packaged by Anaconda, Inc. | (main, Jun 18 2024, 15:03:55) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from softioc import softioc
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/anaconda/lib/python3.12/site-packages/softioc/__init__.py", line 8, in <module>
    from epicscorelibs.ioc import \
  File "/usr/local/anaconda/lib/python3.12/site-packages/epicscorelibs/ioc.py", line 22, in <module>
    pvAccessIOC = ctypes.CDLL(path.get_lib("pvAccessIOC"), mode=ctypes.RTLD_GLOBAL)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/anaconda/lib/python3.12/ctypes/__init__.py", line 379, in __init__
    self._handle = _dlopen(self._name, mode)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: /usr/local/anaconda3-2024.06/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /usr/local/anaconda/lib/python3.12/site-packages/epicscorelibs/lib/libpvAccessIOC.so.7.0.7.99.1)

I renamed the newly installed libstdc++.so.6 so it wouldn't be found, and tried again. Now the module loads but we still see the buffer overflow issue.

$ /usr/local/anaconda/bin/python3
Python 3.12.4 | packaged by Anaconda, Inc. | (main, Jun 18 2024, 15:03:55) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from softioc import softioc
INFO: PVXS QSRV2 is loaded, permitted, and ENABLED.
>>> softioc.devIocStats('test')
*** buffer overflow detected ***: terminated
Aborted (core dumped)

I'm willing to assist on this further. It's not critical that I make it work in this VM but it makes some of my testing easier. Thanks!

@AlexanderWells-diamond
Copy link
Collaborator

Thank you for the information. I believe this issue to be a replica of epics-base/epicscorelibs#32 - it seems epicscorelibs doesn't currently play nicely with the latest GCC compilers and their default macros.

Until there is a proper release, the workaround for you is to install epicscorelibs from its master branch:

pip install git+https://github.com/epics-base/epicscorelibs.git softioc

Please let me know if that works, if so we can close out this issue. Thanks.

Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@prichards-wmko @AlexanderWells-diamond