# Unix Build Error
**URL:** https://discourse.vtk.org/t/unix-build-error/6805
**Category:** Support
**Created:** [October 12, 2021, 1:34am UTC](https://discourse.vtk.org/t/unix-build-error/6805 "2021-10-12T01:34:12Z")
**Posts on this page:** 18
**Page:** 1
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 12, 2021, 1:34am UTC](https://discourse.vtk.org/t/unix-build-error/6805/1 "2021-10-12T01:34:12Z")
Dear Support,
I am getting a cmake error when I try to build on a Centos 7 Box
**– Performing Test CHECK\_HAVE\_STAT64\_STRUCT - Failed**
The failed test shows
/usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/CMakeTmp/src.c:6:36: error: dereferencing pointer to incomplete type ‘struct stat64’
(void)sizeof(((struct stat64 \*)0)-\>st\_atime);
^~
I am using
cmake 3.21.3
gcc 8.1.0
I am not sure how to resolve this. Is anyone able to give me any hints?
thanks
Simon
---
### Author:  [@mwestphal](https://discourse.vtk.org/u/mwestphal)
#### Post date: [October 12, 2021, 7:46am UTC](https://discourse.vtk.org/t/unix-build-error/6805/2 "2021-10-12T07:46:44Z")
@ben.boeckel may have more info
---
### Author:  [@ben.boeckel](https://discourse.vtk.org/u/ben.boeckel)
#### Post date: [October 12, 2021, 6:00pm UTC](https://discourse.vtk.org/t/unix-build-error/6805/3 "2021-10-12T18:00:49Z")
It’s checking if you have `struct stat64` and it says you don’t. Why is this an error? Is there more output that you’re not showing us here?
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 12, 2021, 7:03pm UTC](https://discourse.vtk.org/t/unix-build-error/6805/4 "2021-10-12T19:03:18Z")
Maybe glibc-devel is not installed, does `/usr/include/sys/stat.h` exist?
Have you used this machine to build VTK before, or is this a fresh linux install?
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 13, 2021, 12:31am UTC](https://discourse.vtk.org/t/unix-build-error/6805/5 "2021-10-13T00:31:35Z")
> [@dgobbi](#):
>
> `/usr/include/sys/stat.h`
That file exists : `/usr/include/sys/stat.h`
This is a Centos 7 box.and we have previously compiled vtk/7.0.0-gcc5
The CMAKE output was
> cmake -DCMAKE\_INSTALL\_PREFIX=/usr/local/vtk/9.1.0 -DBUILD\_SHARED\_LIBS=ON -DVTK\_USE\_MPI=ON -DVTK\_WRAP\_PYTHON=ON -DVTK\_PYTHON\_VERSION=3 -DBUILD\_TESTING=ON …
> …
> …
> – Performing Test CHECK\_HAVE\_STAT64\_STRUCT
> – Performing Test CHECK\_HAVE\_STAT64\_STRUCT - Failed
> – Looking for localeconv
> – Looking for localeconv - found
> – Performing Test HAVE\_PTHREAD\_MUTEX\_RECURSIVE\_DEFN
> – Performing Test HAVE\_PTHREAD\_MUTEX\_RECURSIVE\_DEFN - Success
> – Configuring incomplete, errors occurred!
I had assumed the last failure was the cause of the problem, but looking again this may not be the case…I am afraid that as a new user I can not upload files,
Looking up the screen I now notice this…
**– Check size of \_Quad**
**– Check size of \_Quad - failed**
**CMake Error at ThirdParty/hdf5/vtkhdf5/config/cmake/ConfigureChecks.cmake:367 (list):**
\*\* list index: 1 out of range (-1, 0)\*\*
**Call Stack (most recent call first):**
\*\* ThirdParty/hdf5/vtkhdf5/CMakeLists.txt:503 (include)\*\*
The otuput in the error file has this
/\> usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/CheckTypeSize/\_SIZEOF\_\_QUAD.c:28:22: error: ‘\_Quad’ undeclared here
> (not in a function); did you mean ‘u\_quad\_t’?
> #define SIZE (sizeof(\_Quad))
> ^ ~~~~
> /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/CheckTypeSize/\_SIZEOF\_\_QUAD.c:30:12: note: in expansion of macro ‘SI
> ZE’
> (‘0’ + ((SIZE / 10000)%10)),
> ^~~~
Could this be the thing breaking the build?
thanks
Simon
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 13, 2021, 1:01am UTC](https://discourse.vtk.org/t/unix-build-error/6805/6 "2021-10-13T01:01:40Z")
The cmake list index error comes after this inline test runs: [ldbl\_flt128.c](https://discourse.vtk.org/uploads/short-url/joNs1RNRpyoJJfu1Ac0JY60mUse.c) (482 Bytes)
On my machine, this test prints two values: `21;0;` This means ldbl 21 digits, flt128 0 digits.
Can you try compiling and running the attached test on your own machine? I imagine that it should print the same thing.
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 13, 2021, 7:06am UTC](https://discourse.vtk.org/t/unix-build-error/6805/7 "2021-10-13T07:06:26Z")
David
I downloaded the file and it worked
> [smichnow@monarch-login2 build] gcc ldbl\_flt128.c [smichnow@monarch-login2 build] ./a.out
> 21;0;[smichnow@monarch-login2 build]$
We are using
hdf5/1.10.5
Is this a sufficient version for this build?
regards
Simon
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 13, 2021, 12:44pm UTC](https://discourse.vtk.org/t/unix-build-error/6805/8 "2021-10-13T12:44:09Z")
> [@simon.michnowicz](#):
>
> We are using hdf5/1.10.5 Is this a sufficient version for this build?
According to the bits of error log you sent, VTK is building its own internal hdf5 (which is its default) rather than using the hdf5 on your system. (VTK’s internal hdf5 is 1.12.1, I don’t know what version it needs for an external hdf5.)
In any case, the `Check size of _Quad - failed` message is not something to worry about. That particular test fails on my machine, too, but I can build VTK just fine. It’s just the CMake errors that you have to watch for.
It’s odd that the test program prints `21;0;` but CMake complains `list index: 1 out of range`. Are you sure this is the first CMake Error that is printed? When debugging it’s important to go through the errors in order, starting at the top.
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 14, 2021, 4:13am UTC](https://discourse.vtk.org/t/unix-build-error/6805/9 "2021-10-14T04:13:25Z")
David
the first error (it is in red font, and probably the main one breaking cmake) is
**cmake -DCMAKE\_INSTALL\_PREFIX=/usr/local/vtk/9.1.0 -DBUILD\_SHARED\_LIBS=ON -DVTK\_USE\_MPI=ON -DVTK\_WRAP\_PYTHON=ON -DVTK\_PYTHON\_VERSION=3 …**
CMake Error at ThirdParty/hdf5/vtkhdf5/config/cmake/ConfigureChecks.cmake:367 (list):
list index: 1 out of range (-1, 0)
Call Stack (most recent call first):
ThirdParty/hdf5/vtkhdf5/CMakeLists.txt:503 (include)
Since the web page will not let me upload files, could I send you the full error log by some other means?
thanks
Simon
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 14, 2021, 4:36am UTC](https://discourse.vtk.org/t/unix-build-error/6805/10 "2021-10-14T04:36:19Z")
If that’s the first error, then it’s a good place to start, I don’t think the full log would be very enlightening given the information you’ve already sent.
We’ve already run the program that is supposed to provide the input to this list() command that is errorring, and it looks fine. So the next step is to instrument the ConfigureChecks.cmake file to get additional info.
Can you edit the file and add this “print” statement immediately before line 367?
```
message(STATUS "PROG_OUTPUT4: (${PROG_OUTPUT4})")
```
That will give tell us exactly what input is causing the list() command to fail. (There’s probably going to be a few more back-and-forths before we actually get to the root of the problem).
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 14, 2021, 5:13am UTC](https://discourse.vtk.org/t/unix-build-error/6805/11 "2021-10-14T05:13:41Z")
> [@dgobbi](#):
>
> `message(STATUS "PROG_OUTPUT4: (${PROG_OUTPUT4})")`
The output is now
– Check size of \_Quad
– Check size of \_Quad - failed
– PROG\_OUTPUT4: (Segmentation fault)
CMake Error at ThirdParty/hdf5/vtkhdf5/config/cmake/ConfigureChecks.cmake:368 (list):
list index: 1 out of range (-1, 0)
Call Stack (most recent call first):
ThirdParty/hdf5/vtkhdf5/CMakeLists.txt:503 (include)
regards
Simon
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 14, 2021, 6:30am UTC](https://discourse.vtk.org/t/unix-build-error/6805/12 "2021-10-14T06:30:05Z")
That’s interesting. I wonder why the test program segfaults when cmake compiles it, but it ran fine when you compiled it yourself? Maybe cmake is passing bad compiler flags?
In any case, you can substitute the known good output of that program in place of the segfault message. Try putting this immediately after the `message()` line that you just added:
```
set(PROG_OUTPUT4 21 0)
```
This should allow the `list()` command to succeed. Then we’ll know if it was the only issue.
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 14, 2021, 9:18am UTC](https://discourse.vtk.org/t/unix-build-error/6805/13 "2021-10-14T09:18:01Z")
> [@dgobbi](#):
>
> `set(PROG_OUTPUT4 21 0)`
David
that line removed the cmake error. I get a different error when I type make…
[18%] Generating the Python module initialization sources for vtkFiltersParallelMPIPython
make[2]: \*\*\* [CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInit.cxx] Segmentation fault (core dumped)
make[1]: \*\*\* [CMakeFiles/vtkFiltersParallelMPIPython.dir/all] Error 2
I am not that familiar with cmake. Is there any log file for me to see what command was actually being executed?
thanks
Simon
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 14, 2021, 9:41am UTC](https://discourse.vtk.org/t/unix-build-error/6805/14 "2021-10-14T09:41:26Z")
There’s no log file for make, but tell make to show the commands it executes:
```
VERBOSE=1 make vtkFiltersParallelMPIPython
```
In this case, it will be vtkWrapPythonInit-9.1 but it will be interesting to see what args it’s being called with (since the args are making it crash).
One of the args will be this file in the build tree:
```
CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPython-init.data
```
The contents of this file, on my system, are this:
```nohighlight
vtkFiltersParallelMPI
vtkDistributedPointCloudFilter
vtkPExtractGrid
vtkPExtractRectilinearGrid
vtkPExtractVOI
vtkStructuredImplicitConnectivity
vtkFiltersParallelMPIModule
DEPENDS
vtkmodules.vtkCommonCore
vtkmodules.vtkCommonExecutionModel
vtkmodules.vtkCommonSystem
vtkmodules.vtkFiltersExtraction
vtkmodules.vtkImagingCore
```
Can you check to see if the contents are the same on your system?
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 15, 2021, 1:21am UTC](https://discourse.vtk.org/t/unix-build-error/6805/15 "2021-10-15T01:21:54Z")
Hi. The make file yields
> 100%] Generating the Python module initialization sources for vtkFiltersParallelMPIPython
> bin/vtkWrapPythonInit-9.1 /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPython-init.data /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInit.cxx /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInitImpl.cxx
> make[3]: \*\*\* [CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInit.cxx] Segmentation fault (core dumped)
dmesg -T shows
> [Fri Oct 15 11:56:58 2021] vtkWrapPythonIn[20608]: segfault at b8 ip 00007f7a33fc095e sp 00007ffc49dcbd48 error 4 in libc-2.17.so[7f7a33f31000+1c4000]
> [Fri Oct 15 12:17:47 2021] vtkWrapPythonIn[26228]: segfault at b8 ip 00007f8977fbe95e sp 00007ffd7bedf1a8 error 4 in libc-2.17.so[7f8977f2f000+1c4000]
The contents of CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPython-init.data
> vtkFiltersParallelMPI
> vtkDistributedPointCloudFilter
> vtkPExtractGrid
> vtkPExtractRectilinearGrid
> vtkPExtractVOI
> vtkStructuredImplicitConnectivity
> vtkFiltersParallelMPIModule
> DEPENDS
> vtkmodules.vtkCommonCore
> vtkmodules.vtkCommonExecutionModel
> vtkmodules.vtkCommonSystem
> vtkmodules.vtkFiltersExtraction
> vtkmodules.vtkImagingCore
The dmesg commands make me thinks it is a library issue but all other modules (i.e. python, cmake )in the system were built with gcc8 so I am not sure where to begin.
thanks
---
### Author:  [@dgobbi](https://discourse.vtk.org/u/dgobbi)
#### Post date: [October 15, 2021, 2:04am UTC](https://discourse.vtk.org/t/unix-build-error/6805/16 "2021-10-15T02:04:30Z")
Well, it’s vaguely possible that some bits got flipped on disk. You can try `rpm -V` to verify the checksums for the glibc and gcc packages.
For vtkWrapPythonInit-9.1, since its input looks fine and since you have the command line, I think the next step should be to run the command line in gdb and get a stack trace. And if that doesn’t give any useful info, then recompile in debug mode and try the debugger again.
---
### Author:  [@simon.michnowicz](https://discourse.vtk.org/u/simon.michnowicz)
#### Post date: [October 15, 2021, 3:50am UTC](https://discourse.vtk.org/t/unix-build-error/6805/17 "2021-10-15T03:50:59Z")
David
sadly this did not produce any meaningful information. I will try without MPI and see if I can get a single server version going. Maybe try different versions of MPI.
[\> smichnow@monarch-login2 build]$ gdb bin/vtkWrapPythonInit-9.1
> GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-120.el7
> Copyright (C) 2013 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later [http://gnu.org/licenses/gpl.html](http://gnu.org/licenses/gpl.html)
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type “show copying”
> and “show warranty” for details.
> This GDB was configured as “x86\_64-redhat-linux-gnu”.
> For bug reporting instructions, please see:
> [http://www.gnu.org/software/gdb/bugs/](http://www.gnu.org/software/gdb/bugs/)…
> Reading symbols from /usr/local/src/VTK/VTK-9.1.0.rc2/build/bin/vtkWrapPythonInit-9.1…done.
> (gdb) run /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPython-init.data /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInit.cxx /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInitImpl.cxx
> Starting program: /usr/local/src/VTK/VTK-9.1.0.rc2/build/bin/vtkWrapPythonInit-9.1 /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPython-init.data /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInit.cxx /usr/local/src/VTK/VTK-9.1.0.rc2/build/CMakeFiles/vtkFiltersParallelMPIPythonPython/vtkFiltersParallelMPIPythonInitImpl.cxx
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00007ffff7a9c95e in ?? ()
> Missing separate debuginfos, use: debuginfo-install glibc-2.17-324.el7\_9.x86\_64
> (gdb) where
> #0 0x00007ffff7a9c95e in ?? ()
> #1 0x00007ffff7de7b03 in \_dl\_relocate\_object () from /lib64/ld-linux-x86-64.so.2
> #2 0x00007ffff7ddf99a in dl\_main () from /lib64/ld-linux-x86-64.so.2
> #3 0x00007ffff7df300e in \_dl\_sysdep\_start () from /lib64/ld-linux-x86-64.so.2
> #4 0x00007ffff7ddcbd1 in \_dl\_start () from /lib64/ld-linux-x86-64.so.2
> #5 0x00007ffff7ddc148 in \_start () from /lib64/ld-linux-x86-64.so.2
> #6 0x0000000000000004 in ?? ()
> #7 0x00007fffffffd16c in ?? ()
> #8 0x00007fffffffd1ad in ?? ()
> #9 0x00007fffffffd227 in ?? ()
> #10 0x00007fffffffd29f in ?? ()
> #11 0x0000000000000000 in ?? ()
---
### Author:  [@ben.boeckel](https://discourse.vtk.org/u/ben.boeckel)
#### Post date: [October 26, 2021, 10:42pm UTC](https://discourse.vtk.org/t/unix-build-error/6805/18 "2021-10-26T22:42:54Z")
> [@simon.michnowicz](#):
>
> #6 0x0000000000000004 in ?? ()
This seems…bad. However, it is also not actually in VTK’s code (yet?). I think something went very wrong here. Can you run it at the command line with `LD_DEBUG=libs` in the environment? That output should show what libraries it is using.