Ildar,
(1) Ignore the warnings;
(2) Your loader issue with PIC is unusual, you should be able to link to
static libraries without having to mess with this flag or recompile fftw3;
do you have the libfftw3-dev and fftw-dev libraries installed? If not, you
don't have the required headers
and I think that's probably the case here:
sudo apt install libfftw3-dev fftw-dev
(3) If the miniconda fix works for you, great - I avoid it in general due
to a personal aversion to the python/anaconda/etc. multiple versions of
things on my machine BUT if it works for you, do it; and
(4) During install it is not uncommon to see things like you see if the
required packages (I mean the ones you will install via apt) are not
present.
Cheers,
Todd
On Mon, Feb 5, 2024 at 2:36 AM Ildar Garipov <
garipov_ildar_from.tp.bii.a-star.edu.sg> wrote:
> Hi, Todd. Thank you for your response.
>
> For the work desktop seems like I have deeper trouble with GNU compilers
> and repositories, so it's out of further consideration.
>
> Now I've tried to install the AMBER by following your instructions on my
> laptop.
> I can't have a successful configuration of installation with the key -DDOWNLOAD_MINICONDA=FALSE
> , but if it's TRUE *run_cmake* finishes well.
> Further '*sudo make install*' crushes on 14%. The last few rows of its
> output:
>
> [ 14%] Building Fortran object
> AmberTools/src/addles/CMakeFiles/addles.dir/random.F90.o
> [ 14%] Building Fortran object
> AmberTools/src/addles/CMakeFiles/addles.dir/les2prm.F.o
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/les2prm.F:19:2:*
>
> 19 | 30 format (5e16.8)
> | *1*
> *Warning:* Label 30 at *(1)* defined but not used [*-Wunused-label*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/les2prm.F:18:2:*
>
> 18 | 20 format (12i6)
> | *1*
> *Warning:* Label 20 at *(1)* defined but not used [*-Wunused-label*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/les2prm.F:17:2:*
>
> 17 | 15 format (a)
> | *1*
> *Warning:* Label 15 at *(1)* defined but not used [*-Wunused-label*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/les2prm.F:16:2:*
>
> 16 | 10 format (20a4)
> | *1*
> *Warning:* Label 10 at *(1)* defined but not used [*-Wunused-label*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:12:25:*
>
> 12 | integer tb1(maxbnd),tb2(maxbnd),tb3(maxbnd),tb4(maxbnd),
> | *1*
> *Warning:* Array ‘*tb1*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:15:26:*
>
> 15 | . tb10(maxbnd)
> | *1*
> *Warning:* Array ‘*tb10*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure
> unsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursi*
> ve’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concur
> rently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:12:37:*
>
> 12 | integer tb1(maxbnd),tb2(maxbnd),tb3(maxbnd),tb4(maxbnd),
> | *1*
> *Warning:* Array ‘*tb2*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:12:49:*
>
> 12 | integer tb1(maxbnd),tb2(maxbnd),tb3(maxbnd),tb4(maxbnd),
> | *1*
> *Warning:* Array ‘*tb3*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:12:61:*
>
> 12 | integer tb1(maxbnd),tb2(maxbnd),tb3(maxbnd),tb4(maxbnd),
> | *1*
> *Warning:* Array ‘*tb4*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:13:25:*
>
> 13 | . tb5(maxbnd)
> | *1*
> *Warning:* Array ‘*tb5*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:14:25:*
>
> 14 | integer tb6(maxbnd),tb7(maxbnd),tb8(maxbnd),tb9(maxbnd),
> | *1*
> *Warning:* Array ‘*tb6*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:14:37:*
>
> 14 | integer tb6(maxbnd),tb7(maxbnd),tb8(maxbnd),tb9(maxbnd),
> | *1*
> *Warning:* Array ‘*tb7*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:14:49:*
>
> 14 | integer tb6(maxbnd),tb7(maxbnd),tb8(maxbnd),tb9(maxbnd),
> | *1*
> *Warning:* Array ‘*tb8*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:14:61:*
>
> 14 | integer tb6(maxbnd),tb7(maxbnd),tb8(maxbnd),tb9(maxbnd),
> | *1*
> *Warning:* Array ‘*tb9*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:4:25:*
>
> 4 | integer th1(maxbnd),th2(maxbnd),th3(maxbnd),th4(maxbnd),
> | *1*
> *Warning:* Array ‘*th1*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:7:26:*
>
> 7 | . th10(maxbnd)
> | *1*
> *Warning:* Array ‘*th10*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure
> unsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursi*
> ve’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concur
> rently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:4:37:*
>
> 4 | integer th1(maxbnd),th2(maxbnd),th3(maxbnd),th4(maxbnd),
> | *1*
> *Warning:* Array ‘*th2*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:4:49:*
>
> 4 | integer th1(maxbnd),th2(maxbnd),th3(maxbnd),th4(maxbnd),
> | *1*
> *Warning:* Array ‘*th3*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:4:61:*
>
> 4 | integer th1(maxbnd),th2(maxbnd),th3(maxbnd),th4(maxbnd),
> | *1*
> *Warning:* Array ‘*th4*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:5:25:*
>
> 5 | . th5(maxbnd)
> | *1*
> *Warning:* Array ‘*th5*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:6:37:*
>
> 6 | integer th6(maxbnd),th7(maxbnd),th8(maxbnd),th9(maxbnd),
> | *1*
> *Warning:* Array ‘*th7*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:6:49:*
>
> 6 | integer th6(maxbnd),th7(maxbnd),th8(maxbnd),th9(maxbnd),
> | *1*
> *Warning:* Array ‘*th8*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:6:61:*
>
> 6 | integer th6(maxbnd),th7(maxbnd),th8(maxbnd),th9(maxbnd),
> | *1*
> *Warning:* Array ‘*th9*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:16:25:*
>
> 16 | integer tn1(maxbnd),tn2(maxbnd),tn3(maxbnd),tn4(maxbnd),
> | *1*
> *Warning:* Array ‘*tn1*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:19:26:*
>
> 19 | . tn10(maxbnd)
> | *1*
> *Warning:* Array ‘*tn10*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure
> unsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursi*
> ve’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concur
> rently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:16:37:*
>
> 16 | integer tn1(maxbnd),tn2(maxbnd),tn3(maxbnd),tn4(maxbnd),
> | *1*
> *Warning:* Array ‘*tn2*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:16:49:*
>
> 16 | integer tn1(maxbnd),tn2(maxbnd),tn3(maxbnd),tn4(maxbnd),
> | *1*
> *Warning:* Array ‘*tn3*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:16:61:*
>
> 16 | integer tn1(maxbnd),tn2(maxbnd),tn3(maxbnd),tn4(maxbnd),
> | *1*
> *Warning:* Array ‘*tn4*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:17:25:*
>
> 17 | . tn5(maxbnd)
> | *1*
> *Warning:* Array ‘*tn5*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:18:37:*
>
> 18 | integer tn6(maxbnd),tn7(maxbnd),tn8(maxbnd),tn9(maxbnd),
> | *1*
> *Warning:* Array ‘*tn7*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:18:49:*
>
> 18 | integer tn6(maxbnd),tn7(maxbnd),tn8(maxbnd),tn9(maxbnd),
> | *1*
> *Warning:* Array ‘*tn8*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:18:61:*
>
> 18 | integer tn6(maxbnd),tn7(maxbnd),tn8(maxbnd),tn9(maxbnd),
> | *1*
> *Warning:* Array ‘*tn9*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:8:25:*
>
> 8 | integer tp1(maxbnd),tp2(maxbnd),tp3(maxbnd),tp4(maxbnd),
> | *1*
> *Warning:* Array ‘*tp1*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:11:26:*
>
> 11 | . tp10(maxbnd)
> | *1*
> *Warning:* Array ‘*tp10*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure
> unsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursi*
> ve’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concur
> rently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:8:37:*
>
> 8 | integer tp1(maxbnd),tp2(maxbnd),tp3(maxbnd),tp4(maxbnd),
> | *1*
> *Warning:* Array ‘*tp2*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:8:49:*
>
> 8 | integer tp1(maxbnd),tp2(maxbnd),tp3(maxbnd),tp4(maxbnd),
> | *1*
> *Warning:* Array ‘*tp3*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:8:61:*
>
> 8 | integer tp1(maxbnd),tp2(maxbnd),tp3(maxbnd),tp4(maxbnd),
> | *1*
> *Warning:* Array ‘*tp4*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:9:25:*
>
> 9 | . tp5(maxbnd)
> | *1*
> *Warning:* Array ‘*tp5*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:10:25:*
>
> 10 | integer tp6(maxbnd),tp7(maxbnd),tp8(maxbnd),tp9(maxbnd),
> | *1*
> *Warning:* Array ‘*tp6*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:10:37:*
>
> 10 | integer tp6(maxbnd),tp7(maxbnd),tp8(maxbnd),tp9(maxbnd),
> | *1*
> *Warning:* Array ‘*tp7*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:10:49:*
>
> 10 | integer tp6(maxbnd),tp7(maxbnd),tp8(maxbnd),tp9(maxbnd),
> | *1*
> *Warning:* Array ‘*tp8*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/TEMP.h:10:61:*
>
> 10 | integer tp6(maxbnd),tp7(maxbnd),tp8(maxbnd),tp9(maxbnd),
> | *1*
> *Warning:* Array ‘*tp9*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedure u
> nsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘
> *-frecursiv*
> e’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed concurr
> ently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> [ 14%] Building Fortran object
> AmberTools/src/addles/CMakeFiles/addles.dir/checksz.F.o
> [ 14%] Building Fortran object
> AmberTools/src/addles/CMakeFiles/addles.dir/addspace_atm1st.F.o
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/MISC.h:33:66:*
>
> 33 | integer revpoint(maxnatom),ipick(maxnatom),poiatom(maxnatom)
> |
> *1*
> *Warning:* Array ‘*poiatom*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the procedu
> re unsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘*-frecu*
> rsive’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change the
> code to use an ALLOCATABLE array. If the variable is never accessed con
> currently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> */home/qwezxc8/software/amber22_src/AmberTools/src/addles/MISC.h:33:32:*
>
> 33 | integer revpoint(maxnatom),ipick(maxnatom),poiatom(maxnatom)
> | *1*
> *Warning:* Array ‘*revpoint*’ at *(1)* is larger than limit set by ‘
> *-fmax-stack-var-size=*’, moved from stack to static storage. This makes
> the proced
> ure unsafe when called recursively, or concurrently from multiple threads.
> Consider increasing the ‘*-fmax-stack-var-size=*’ limit (or use ‘*-frec*
> ursive’, which implies unlimited ‘*-fmax-stack-var-size*’) - or change
> the code to use an ALLOCATABLE array. If the variable is never accessed co
> ncurrently, this warning can be ignored, and the variable could also be
> declared with the SAVE attribute. [*-Wsurprising*]
> [ 14%] *Linking Fortran executable addles*
> [ 14%] Built target addles
> [ 14%] Building CXX object
> AmberTools/src/cew/CMakeFiles/libcew.dir/Ewald.cpp.o
> */home/qwezxc8/software/amber22_src/AmberTools/src/cew/Ewald.cpp:* In
> destructor ‘*cew::Ewald::~Ewald()*’:
> */home/qwezxc8/software/amber22_src/AmberTools/src/cew/Ewald.cpp:565:49:* *warning:
> *dereferencing type-punned pointer will break strict-aliasing r
> ules [*-Wstrict-aliasing*]
> 565 | fftw_free(reinterpret_cast< fftw_complex * &>(*dftcoef*));
> | *^~~~~~~*
> [ 14%] Building CXX object
> AmberTools/src/cew/CMakeFiles/libcew.dir/iface.cpp.o
> [ 14%] *Linking CXX shared library libcew.so*
> /usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): warning: relocation
> against `stdout@@GLIBC_2.2.5' in read-only section `.text'
> /usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32
> against symbol `stdout..GLIBC_2.2.5' can not be used when making a s
> hared object; recompile with -fPIC
> /usr/bin/ld: final link failed: bad value
> collect2: error: ld returned 1 exit status
> make[2]: *** [AmberTools/src/cew/CMakeFiles/libcew.dir/build.make:114:
> AmberTools/src/cew/libcew.so] Error 1
> make[1]: *** [CMakeFiles/Makefile2:5851:
> AmberTools/src/cew/CMakeFiles/libcew.dir/all] Error 2
> make: *** [Makefile:156: all] Error 2
>
>
> ------------------------------
> *From:* Todd Minehardt <todd.minehardt.gmail.com>
> *Sent:* Tuesday, January 30, 2024 11:14 PM
> *To:* Ildar Garipov <garipov_ildar_from.tp.bii.a-star.edu.sg>; AMBER
> Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] AMBER22 and AmberTools23 installation issue
>
> This email is from a sender external to A*STAR. If you are unsure of the
> content, please check the source before you respond.
>
> Ildar,
>
> (1) sudo apt install libchemistry-mol-perl
>
> (2) Try this as your run_cmake, note you will have to make install with
> sudo otherwise change -DCMAKE_INSTALL_PREFIX but be sure to keep the
> additional 2 flags I have here:
>
> cmake $AMBER_PREFIX/amber22_src \
> -DCMAKE_INSTALL_PREFIX=/usr/local/amber22 \
> -DCOMPILER=GNU \
> -DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=FALSE -DAPPLY_UPDATES=TRUE \
> -DTRUST_SYSTEM_LIBS=TRUE \
> 2>&1 | tee cmake.log
>
> (3) Report back.
>
> Cheers,
>
> Todd
>
> On Tue, Jan 30, 2024 at 3:10 AM Ildar Garipov via AMBER <amber.ambermd.org>
> wrote:
>
> Dear developers and users,
>
> I tried to install AMBER from source on my laptop and work desktop. Both
> times I followed the 2023 Reference Manual and had partially similar
> problems with the Perl module Chemistry. I've included for you the details
> of my systems and the corresponding cmake error output. Thanks in advance.
>
>
>
> Both installations were performed with the same cmake keys below.
> run_cmake content:
> cmake $AMBER_PREFIX/amber22_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
> -DCOMPILER=GNU \
> -DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE \
> 2>&1 | tee cmake.log
>
>
>
>
> 1. Work desktop.
>
> OS and compiler's version:
> OS: Ubuntu 22.04.3 LTS
> gcc (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
> g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
> GNU Fortran (Ubuntu 10.3.0-15ubuntu1) 10.3.0
> cmake version 3.22.1
> nvcc: Cuda compilation tools, release 11.5, V11.5.119
>
> CMakeError.log:
> Performing C SOURCE FILE Test CMath_LINKS_WITHOUT_M failed with the
> following output:
> Change Dir: /scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_9bc1e/fast &&
> /usr/bin/gmake -f CMakeFiles/cmTC_9bc1e.dir/build.make
> CMakeFiles/cmTC_9bc1e.dir/build
> gmake[1]: Entering directory
> '/scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_9bc1e.dir/src.c.o
> /usr/bin/gcc -DCMath_LINKS_WITHOUT_M -fPIE -std=gnu99 -o
> CMakeFiles/cmTC_9bc1e.dir/src.c.o -c
> /scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp/src.c
> Linking C executable cmTC_9bc1e
> /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_9bc1e.dir/link.txt
> --verbose=1
> /usr/bin/gcc CMakeFiles/cmTC_9bc1e.dir/src.c.o -o cmTC_9bc1e
> /usr/bin/ld: CMakeFiles/cmTC_9bc1e.dir/src.c.o: in function `main':
> src.c:(.text+0x2c): undefined reference to `sin'
> collect2: error: ld returned 1 exit status
> gmake[1]: *** [CMakeFiles/cmTC_9bc1e.dir/build.make:99: cmTC_9bc1e] Error 1
> gmake[1]: Leaving directory
> '/scratch/ildar/software/amber22_src/build/CMakeFiles/CMakeTmp'
> gmake: *** [Makefile:127: cmTC_9bc1e/fast] Error 2
>
>
> Source file was:
> #include <math.h>
>
> int main(int argc, char** argv)
> {
> return sin(argc - 1);
> }
> Determining if the Perl module Chemistry::Mol exists failed with the
> following error output:
> Can't locate Chemistry/Mol.pm in @INC (you may need to install the
> Chemistry::Mol module) (.INC contains: /etc/perl
> /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0
> /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5
> /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34
> /usr/share/perl/5.34 /usr/local/lib/site_perl) at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
>
>
> 1. Personal laptop
>
> OS and compiler's version:
> OS: Kubuntu 22.04.3 LTS
> gcc (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
> g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
> GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
> cmake version 3.22.1
> nvcc: Cuda compilation tools, release 11.5, V11.5.119
>
> CMakeError.log:
> Determining if the Perl module Chemistry::Mol exists failed with the
> following error output:
> Can't locate Chemistry/Mol.pm in @INC (you may need to install the
> Chemistry::Mol module) (.INC contains: /etc/perl
> /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0
> /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5
> /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34
> /usr/share/perl/5.34 /usr/local/lib/site_perl) at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
> This e-mail and any attachments are only for the use of the intended
> recipient and may contain material that is confidential, privileged and/or
> protected by the Official Secrets Act. If you are not the intended
> recipient, please delete it or notify the sender immediately. Please do not
> copy or use it for any purpose or disclose the contents to any other person.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> This e-mail and any attachments are only for the use of the intended
> recipient and may contain material that is confidential, privileged and/or
> protected by the Official Secrets Act. If you are not the intended
> recipient, please delete it or notify the sender immediately. Please do not
> copy or use it for any purpose or disclose the contents to any other
> person.
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 05 2024 - 08:00:02 PST
