# Build fails in vtkExodus on Linux

**URL:** <https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018>\
**Category:** Development\
**Tags:** build\
**Created:** [June 14, 2020, 12:42pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018 "2020-06-14T12:42:35Z")\
**Posts on this page:** 14\
**Page:** 1

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 14, 2020, 12:42pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/1 "2020-06-14T12:42:35Z")

</div>

Hello,

After today’s pull, build fails on Linux with these messages :

> /usr/bin/ld: CMakeFiles/vtkexodusII.dir/src/ex\_open\_par.c.o:(.rodata+0x0): multiple definition of `exodus\_unused\_symbol\_dummy\_1’; CMakeFiles/vtkexodusII.dir/src/ex\_create\_par.c.o:(.rodata+0x0): first defined here  
> collect2: error: ld returned 1 exit status  
> make[6]: \*\*\* [ThirdParty/exodusII/vtkexodusII/CMakeFiles/vtkexodusII.dir/build.make:4172: lib/libvtkexodusII-8.2.so.1] Error 1  
> make[5]: \*\*\* [CMakeFiles/Makefile2:8028: ThirdParty/exodusII/vtkexodusII/CMakeFiles/vtkexodusII.dir/all] Error 2  
> make[5]: \*\*\* Waiting for unfinished jobs…  
> make[4]: \*\*\* [Makefile:150: all] Error 2  
> make[3]: \*\*\* [CMakeFiles/VTK.dir/build.make:137: VTK-prefix/src/VTK-stamp/VTK-build] Error 2  
> make[2]: \*\*\* [CMakeFiles/Makefile2:1115: CMakeFiles/VTK.dir/all] Error 2  
> make[1]: \*\*\* [CMakeFiles/Makefile2:224: CMakeFiles/Slicer.dir/rule] Error 2

In hope of a fix,

Regards.

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 14, 2020, 3:03pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/2 "2020-06-14T15:03:25Z")

</div>

If this was not a completely clear build (you updated an existing build tree) then please delete the entire top-level build directory of Slicer and start a new build.

---

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 14, 2020, 3:41pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/3 "2020-06-14T15:41:50Z")

</div>

It was indeed a clean build, I forgot this important detail.

Configured and built as such :

> export CFLAGS=“-I/usr/include/tirpc”  
> export CXXFLAGS=“-I/usr/include/tirpc”  
> cmake -DSlicer\_VTK\_VERSION\_MAJOR:INT=8 -DQt5\_DIR:PATH=/usr/lib/cmake/Qt5 -DBUILD\_TESTING:BOOL=OFF -DCMAKE\_BUILD\_TYPE:STRING=Release -DADDITIONAL\_CXX\_FLAGS:STRING=-I/usr/include/tirpc …/Slicer  
> export LANG=C  
> export LC\_ALL=C  
> make -j6

The ‘tirpc’ path is specific to Arch.  
Using GCC 10.1.0, Qt 5.15.0.

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 14, 2020, 4:07pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/4 "2020-06-14T16:07:41Z")

</div>

It looks like an error caused by gcc tightening some restrictions - [https://gitlab.kitware.com/vtk/vtk/-/issues/17774](https://gitlab.kitware.com/vtk/vtk/-/issues/17774)

We plan to upgrade to latest VTK soon. That version will contain the fix. @jcfr do you have an estimation of when the update may happen?

In the meantime, you may backport the fix to Slicer’s VTK or use an older gcc version.

---

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 14, 2020, 8:41pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/5 "2020-06-14T20:41:36Z")

</div>

After backporting the available patch to Slicer’s VTK, the build process completes successfully.

For the record, it fails to build after downgrading GCC to 9.2; I suppose it’s related to the GCC version that built Arch’s currently installed libraries.

Thanks.

-\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*-

> /usr/bin/ld: /usr/lib/libQt5Widgets.so.5.15.0: undefined reference to `std::pmr::monotonic_buffer_resource::~monotonic_buffer_resource()@GLIBCXX_3.4.28' /usr/bin/ld: /usr/lib/libQt5Widgets.so.5.15.0: undefined reference to `vtable for std::pmr::monotonic\_buffer\_resource@GLIBCXX\_3.4.28’  
> collect2: error: ld returned 1 exit status  
> make[6]: \*\*\* [CMakeFiles/CTKAppLauncher.dir/build.make:109: bin/CTKAppLauncher] Error 1  
> make[5]: \*\*\* [CMakeFiles/Makefile2:227: CMakeFiles/CTKAppLauncher.dir/all] Error 2  
> make[4]: \*\*\* [Makefile:172: all] Error 2  
> make[3]: \*\*\* [CMakeFiles/CTKAppLauncherLib.dir/build.make:134: CTKAppLauncherLib-prefix/src/CTKAppLauncherLib-stamp/CTKAppLauncherLib-build] Error 2  
> make[2]: \*\*\* [CMakeFiles/Makefile2:493: CMakeFiles/CTKAppLauncherLib.dir/all] Error 2  
> make[2]: \*\*\* Waiting for unfinished jobs…  
> Note: switching to ‘3.30.1’.

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 14, 2020, 9:26pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/6 "2020-06-14T21:26:57Z")

</div>

Great, thanks for the update. Could you send a pull request to Slicer’s VTK with the backported fix?

---

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 14, 2020, 9:50pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/7 "2020-06-14T21:50:10Z")

</div>

This diff is easily obtained, but never did a pull request anywhere. Anyway, I 'll investigate ASAP, in daylight.

---

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 15, 2020, 10:40am UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/8 "2020-06-15T10:40:37Z")

</div>

The PR process is too heavy for such a trivial patch, I’m posting it here. Anyway, it follows the one you [mentioned](https://gitlab.kitware.com/vtk/vtk/-/issues/17774).

```
diff --git a/ThirdParty/exodusII/update.sh b/ThirdParty/exodusII/update.sh
index 21b1098191..db2450250a 100755
--- a/ThirdParty/exodusII/update.sh
+++ b/ThirdParty/exodusII/update.sh
@@ -8,7 +8,7 @@ readonly name="exodusII"
 readonly ownership="Seacas Upstream <kwrobot@kitware.com>"
 readonly subtree="ThirdParty/$name/vtk$name"
 readonly repo="https://gitlab.kitware.com/third-party/seacas.git"
-readonly tag="for/vtk-old"
+readonly tag="for/vtk-20200128-7.24f-v2019-12-18"
 readonly paths="
 packages/seacas/libraries/exodus/CMakeLists.vtk.txt
 packages/seacas/libraries/exodus/cmake/exodus_config.h.in
diff --git a/ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c b/ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c
index bf5bb44711..1286074fac 100644
--- a/ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c
+++ b/ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c
@@ -614,5 +614,5 @@ int ex_create_par_int(const char *path, int cmode, int *comp_ws, int *io_ws, MPI
  * Prevent warning in some versions of ranlib(1) because the object
  * file has no symbols.
  */
-const char exodus_unused_symbol_dummy_1;
+const char exodus_unused_symbol_dummy_ex_create_par;
 #endif
diff --git a/ThirdParty/exodusII/vtkexodusII/src/ex_open_par.c b/ThirdParty/exodusII/vtkexodusII/src/ex_open_par.c
index f379fc3496..c568353f52 100644
--- a/ThirdParty/exodusII/vtkexodusII/src/ex_open_par.c
+++ b/ThirdParty/exodusII/vtkexodusII/src/ex_open_par.c
@@ -474,5 +474,5 @@ int ex_open_par_int(const char *path, int mode, int *comp_ws, int *io_ws, float
  * Prevent warning in some versions of ranlib(1) because the object
  * file has no symbols.
  */
-const char exodus_unused_symbol_dummy_1;
+const char exodus_unused_symbol_dummy_ex_open_par;
 #endif
```

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [June 15, 2020, 9:47pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/9 "2020-06-15T21:47:25Z")

</div>

Thanks for the patch.

In fact, this is much simpler.

Could you fork [https://github.com/Slicer/VTK](https://github.com/Slicer/VTK) ? And publish a Pull Request against the Slicer fork that based on [https://github.com/Slicer/VTK/tree/slicer-v8.2.0-2018-10-02-74d9488523](https://github.com/Slicer/VTK/tree/slicer-v8.2.0-2018-10-02-74d9488523) adding the commit ? Once this is done, we will take care of integrating it and updating Slicer.

Thanks for your help 🙏

To learn more about the Slicer fork, read here: [https://github.com/Slicer/VTK](https://github.com/Slicer/VTK)

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 16, 2020, 2:42am UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/10 "2020-06-16T02:42:07Z")

</div>

@jcfr I find the process described here quite complicated, too. My impression is that a new branch has to be created for each pull request, but it is not clear why or how exactly it should be named.

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [June 16, 2020, 1:05pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/11 "2020-06-16T13:05:23Z")

</div>

@lassoan Here is a pull request adding “How to backport changes to a specific branch ?” section to the README. See [README: Add "How to backport changes to a specific branch ?" by jcfr · Pull Request #27 · Slicer/VTK · GitHub](https://github.com/Slicer/VTK/pull/27)

> My impression is that a new branch has to be created for each pull request

The introduction of this new README entry should help clarify

> it is not clear why or how exactly it should be named

The branch is named after the commit common to both the upstream project and the Slicer fork. It allows to clearly identify the divergence point.

---

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 16, 2020, 3:07pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/12 "2020-06-16T15:07:47Z")

</div>

The pull request is [visible](https://github.com/Slicer/VTK/pull/28). I hope it’s rightly done, for something new to me.

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [June 17, 2020, 2:47am UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/13 "2020-06-17T02:47:16Z")

</div>

Thanks. Both Slicer/VTK fork and Slicer have been updated.  
For reference, see [https://github.com/Slicer/Slicer/pull/4990](https://github.com/Slicer/Slicer/pull/4990)

---

<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [June 22, 2020, 5:46pm UTC](https://discourse.slicer.org/t/build-fails-in-vtkexodus-on-linux/12018/14 "2020-06-22T17:46:54Z")

</div>

Amongst the many [changes](https://gcc.gnu.org/gcc-10/changes.html) in GCC 10, the use of -fno-common by default explains this behaviour. The fix is therefore valid, moreover explained [here](https://wiki.gentoo.org/wiki/Gcc_10_porting_notes/fno_common); except that I don’t know the effect of the ‘tags’ change in the patch.

I am seeing linking issues with GCC 10, despite the patch now, reported [here](https://discourse.slicer.org/t/build-fails-in-vtk-many-undefined-references/12150). Going with clang for now.