Avogadro trunk

Development
1

Hi all.

I am certainly not the only Mac user of Avogadro, but I have
a problem.

On an Intel Macbook, Avo compiles flawlessly. When I try
to read an older file, I systematically get
"Reading molecular file failed".

Eingen2, openbabel and avogadro were updated to
latest svn versions, in that order.

Any hints ?

Louis

2

On Dec 17, 2008, at 3:21 PM, Louis Ricard wrote:

On an Intel Macbook, Avo compiles flawlessly. When I try
to read an older file, I systematically get
“Reading molecular file failed”.

Eingen2, openbabel and avogadro were updated to
latest svn versions, in that order.

I’m currently using OB-2.2.x branch, not trunk. So it’s possible that
this exists in OB trunk, not the stable branch.

In any case, this is likely a babel issue.

babel -osmi

Does this give you a SMILES back?

Thanks,
-Geoff

3

If I undesrstoo correctly, this command gives:

"babel cysteine.xyz -osmi
C@H(CS)N _(2S)-2-Amino-3-sulfanylpropanoic acid
1 molecule converted
37 audit log messages "

Louis

Le 17 déc. 08 à 21:40, Geoffrey Hutchison a écrit :

On Dec 17, 2008, at 3:21 PM, Louis Ricard wrote:

On an Intel Macbook, Avo compiles flawlessly. When I try
to read an older file, I systematically get
“Reading molecular file failed”.

Eingen2, openbabel and avogadro were updated to
latest svn versions, in that order.

I’m currently using OB-2.2.x branch, not trunk. So it’s possible that
this exists in OB trunk, not the stable branch.

In any case, this is likely a babel issue.

babel -osmi

Does this give you a SMILES back?

Thanks,
-Geoff

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4

Geoff.

After deleting all libs and includes (avogadro and openbabel),
installing OB-2.2.0 and avogadro trunk 1800, everything works
O.K. on my Macbook.

I am really impressed by the rendering speed of orbitals.
Marcus did a great job!

On the G5 side, still is a problem. SVN version 1813,
OB stable. Compile error :

"Linking CXX shared module liborbitalextension.so
Undefined symbols:
“_posix_memalign”, referenced from:
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in
slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>
::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in
slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>
::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in
slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>
::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in
slaterset.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/extensions/liborbitalextension.so] Error 1
make[1]: *** [libavogadro/src/extensions/CMakeFiles/
orbitalextension.dir/all] Error 2
make: *** [all] Error 2"

A problem for Benoit?

Cheers,

Louis

Le 17 déc. 08 à 21:40, Geoffrey Hutchison a écrit :

On Dec 17, 2008, at 3:21 PM, Louis Ricard wrote:

On an Intel Macbook, Avo compiles flawlessly. When I try
to read an older file, I systematically get
“Reading molecular file failed”.

Eingen2, openbabel and avogadro were updated to
latest svn versions, in that order.

I’m currently using OB-2.2.x branch, not trunk. So it’s possible that
this exists in OB trunk, not the stable branch.

In any case, this is likely a babel issue.

babel -osmi

Does this give you a SMILES back?

Thanks,
-Geoff

SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
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5

On Thursday 18 December 2008 14:03:03 Louis Ricard wrote:

Geoff.

After deleting all libs and includes (avogadro and openbabel),
installing OB-2.2.0 and avogadro trunk 1800, everything works
O.K. on my Macbook.

I am really impressed by the rendering speed of orbitals.
Marcus did a great job!

Thanks - they can still go faster but I am very happy with them right now. I
rewrote all of the code to generate them and rethought some of the logic.

On the G5 side, still is a problem. SVN version 1813,
OB stable. Compile error :

"Linking CXX shared module liborbitalextension.so
Undefined symbols:
“_posix_memalign”, referenced from:
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/extensions/liborbitalextension.so] Error 1
make[1]: *** [libavogadro/src/extensions/CMakeFiles/
orbitalextension.dir/all] Error 2
make: *** [all] Error 2"

A problem for Benoit?

This is the new SlaterSet stuff. A lot has changed and so it could be worth
updating Eigen2 if you haven’t already. Otherwise this does look like a job
for Benoit. May be some additional checks as it looks like Eigen is using
“_posix_memalign” and your compiler does not have that symbol.

6

Indeed, we just had to find a replacement for posix_memalign for MSVC
… now it looks like we need a replacement here too!

Please tell me what equivalent function your platform has (hint, on
windows it was called _aligned_malloc).

Cheers,
Benoit

2008/12/18 Marcus D. Hanwell marcus@cryos.org:

On Thursday 18 December 2008 14:03:03 Louis Ricard wrote:

Geoff.

After deleting all libs and includes (avogadro and openbabel),
installing OB-2.2.0 and avogadro trunk 1800, everything works
O.K. on my Macbook.

I am really impressed by the rendering speed of orbitals.
Marcus did a great job!

Thanks - they can still go faster but I am very happy with them right now. I
rewrote all of the code to generate them and rethought some of the logic.

On the G5 side, still is a problem. SVN version 1813,
OB stable. Compile error :

"Linking CXX shared module liborbitalextension.so
Undefined symbols:
“_posix_memalign”, referenced from:
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/extensions/liborbitalextension.so] Error 1
make[1]: *** [libavogadro/src/extensions/CMakeFiles/
orbitalextension.dir/all] Error 2
make: *** [all] Error 2"

A problem for Benoit?

This is the new SlaterSet stuff. A lot has changed and so it could be worth
updating Eigen2 if you haven’t already. Otherwise this does look like a job
for Benoit. May be some additional checks as it looks like Eigen is using
“_posix_memalign” and your compiler does not have that symbol.

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7

hi,

I think this issue is now fixed (rev 899025). Does anyone with OSX can confirm ?

cheers,
Gael.

On Thu, Dec 18, 2008 at 9:21 PM, Benoit Jacob jacob.benoit.1@gmail.com wrote:

Indeed, we just had to find a replacement for posix_memalign for MSVC
… now it looks like we need a replacement here too!

Please tell me what equivalent function your platform has (hint, on
windows it was called _aligned_malloc).

Cheers,
Benoit

2008/12/18 Marcus D. Hanwell marcus@cryos.org:

On Thursday 18 December 2008 14:03:03 Louis Ricard wrote:

Geoff.

After deleting all libs and includes (avogadro and openbabel),
installing OB-2.2.0 and avogadro trunk 1800, everything works
O.K. on my Macbook.

I am really impressed by the rendering speed of orbitals.
Marcus did a great job!

Thanks - they can still go faster but I am very happy with them right now. I
rewrote all of the code to generate them and rethought some of the logic.

On the G5 side, still is a problem. SVN version 1813,
OB stable. Compile error :

"Linking CXX shared module liborbitalextension.so
Undefined symbols:
“_posix_memalign”, referenced from:
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
Eigen::LU<Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000>

::LU(Eigen::Matrix<double, 10000, 10000, 0, 10000, 10000> const&)in

slaterset.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/extensions/liborbitalextension.so] Error 1
make[1]: *** [libavogadro/src/extensions/CMakeFiles/
orbitalextension.dir/all] Error 2
make: *** [all] Error 2"

A problem for Benoit?

This is the new SlaterSet stuff. A lot has changed and so it could be worth
updating Eigen2 if you haven’t already. Otherwise this does look like a job
for Benoit. May be some additional checks as it looks like Eigen is using
“_posix_memalign” and your compiler does not have that symbol.

SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
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pave the way to the Next Web now. Learn more and register at
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