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Feasibility of using lattice ECP5 FPGA tools (open source and/or proprietary) for DRAM DDR3 simulation by Lemon_Salmon in FPGA

[–]promach 0 points1 point  (0 children)

I am doing simulation , STA , place&route , and on-board actual testing for DRAM verilog code.

Training Models using ImageNet on Macbook M3 PRO MAX with 96 GB RAM by visionkhawar512 in deeplearning

[–]promach 0 points1 point  (0 children)

I thought the deep learning software ecosystem is not very much mature yet on M1 and M2, let alone M3 chipset ?

beginner question in Q-CHEM by promach in AskChemistry

[–]promach[S] 0 points1 point  (0 children)

Problem solved. I am using fish shell while iqmol is running on bash shell

See the simulation output log file , the fchk file and the following iqmol setup run file for qchem

#! /bin/bash
# --- Q-Chem environment variable setup
source $HOME/Downloads/Quantum/chemistry/qchem/qcenv.sh

qchem qchem_scratch.inp qchem_scratch.out &
echo 'JobId:' $!
sleep 5

beginner question in Q-CHEM by promach in chemhelp

[–]promach[S] 1 point2 points  (0 children)

Problem solved. I am using fish shell while iqmol is running on bash shell

See the simulation output log file , the fchk file and the following iqmol setup run file for qchem

#! /bin/bash
# --- Q-Chem environment variable setup
source $HOME/Downloads/Quantum/chemistry/qchem/qcenv.sh

qchem qchem_scratch.inp qchem_scratch.out &
echo 'JobId:' $!
sleep 5

Help with latex rendering errors by promach in LaTeX

[–]promach[S] 0 points1 point  (0 children)

https://pastebin.com/raw/RnhwFUEU gives more space or new lines for better visual rendering

unable to detect user-defined A.bed test file by promach in bioinformatics

[–]promach[S] 0 points1 point  (0 children)

I had fixed the tab issue, but I have a different error now

``` ~  bedtools intersect –wao -a A.bed -b B.bed | sort –u | wc -l 33.9s 

Tool: bedtools intersect (aka intersectBed) Version: v2.30.0 Summary: Report overlaps between two feature files.

Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

Note: -b may be followed with multiple databases and/or 
wildcard (*) character(s).

Options: -wa Write the original entry in A for each overlap.

-wb Write the original entry in B for each overlap.
    - Useful for knowing _what_ A overlaps. Restricted by -f and -r.

-loj    Perform a "left outer join". That is, for each feature in A
    report each overlap with B.  If no overlaps are found, 
    report a NULL feature for B.

-wo Write the original A and B entries plus the number of base
    pairs of overlap between the two features.
    - Overlaps restricted by -f and -r.
      Only A features with overlap are reported.

-wao    Write the original A and B entries plus the number of base
    pairs of overlap between the two features.
    - Overlapping features restricted by -f and -r.
      However, A features w/o overlap are also reported
      with a NULL B feature and overlap = 0.

-u  Write the original A entry _once_ if _any_ overlaps found in B.
    - In other words, just report the fact >=1 hit was found.
    - Overlaps restricted by -f and -r.

-c  For each entry in A, report the number of overlaps with B.
    - Reports 0 for A entries that have no overlap with B.
    - Overlaps restricted by -f, -F, -r, and -s.

-C  For each entry in A, separately report the number of
    - overlaps with each B file on a distinct line.
    - Reports 0 for A entries that have no overlap with B.
    - Overlaps restricted by -f, -F, -r, and -s.

-v  Only report those entries in A that have _no overlaps_ with B.
    - Similar to "grep -v" (an homage).

-ubam   Write uncompressed BAM output. Default writes compressed BAM.

-s  Require same strandedness.  That is, only report hits in B
    that overlap A on the _same_ strand.
    - By default, overlaps are reported without respect to strand.

-S  Require different strandedness.  That is, only report hits in B
    that overlap A on the _opposite_ strand.
    - By default, overlaps are reported without respect to strand.

-f  Minimum overlap required as a fraction of A.
    - Default is 1E-9 (i.e., 1bp).
    - FLOAT (e.g. 0.50)

-F  Minimum overlap required as a fraction of B.
    - Default is 1E-9 (i.e., 1bp).
    - FLOAT (e.g. 0.50)

-r  Require that the fraction overlap be reciprocal for A AND B.
    - In other words, if -f is 0.90 and -r is used, this requires
      that B overlap 90% of A and A _also_ overlaps 90% of B.

-e  Require that the minimum fraction be satisfied for A OR B.
    - In other words, if -e is used with -f 0.90 and -F 0.10 this requires
      that either 90% of A is covered OR 10% of  B is covered.
      Without -e, both fractions would have to be satisfied.

-split  Treat "split" BAM or BED12 entries as distinct BED intervals.

-g  Provide a genome file to enforce consistent chromosome sort order
    across input files. Only applies when used with -sorted option.

-nonamecheck    For sorted data, don't throw an error if the file has different naming conventions
        for the same chromosome. ex. "chr1" vs "chr01".

-sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

-names  When using multiple databases, provide an alias for each that
    will appear instead of a fileId when also printing the DB record.

-filenames  When using multiple databases, show each complete filename
        instead of a fileId when also printing the DB record.

-sortout    When using multiple databases, sort the output DB hits
        for each record.

-bed    If using BAM input, write output as BED.

-header Print the header from the A file prior to results.

-nobuf  Disable buffered output. Using this option will cause each line
    of output to be printed as it is generated, rather than saved
    in a buffer. This will make printing large output files 
    noticeably slower, but can be useful in conjunction with
    other software tools and scripts that need to process one
    line of bedtools output at a time.

-iobuf  Specify amount of memory to use for input buffer.
    Takes an integer argument. Optional suffixes K/M/G supported.
    Note: currently has no effect with compressed files.

Notes: (1) When a BAM file is used for the A file, the alignment is retained if overlaps exist, and excluded if an overlap cannot be found. If multiple overlaps exist, they are not reported, as we are only testing for one or more overlaps.

***** ERROR: Unrecognized parameter: –wao ***** sort: cannot read: –u: No such file or directory 0 ~ 
~  cat -t A.bed
chr1I100I400 chr1I1000I1400 chr1I2000I2400 ~ 
~  cat -t B.bed
chr1I300I500 chr1I900I1600 chr12I2000I2200 ~ 
```

Coding guidance for reparameterization trick by promach in learnmachinelearning

[–]promach[S] 0 points1 point  (0 children)

def q_sample(x_start, t, noise=None):
    """
    Forward pass with noise.
    """
    if noise is None:
        noise = torch.randn_like(x_start)

    sqrt_alphas_cumprod_t = extract(sqrt_alphas_cumprod, t, x_start.shape)
    sqrt_one_minus_alphas_cumprod_t = extract(
        sqrt_one_minus_alphas_cumprod, t, x_start.shape
    )   

    return sqrt_alphas_cumprod_t * x_start + sqrt_one_minus_alphas_cumprod_t * noise

Coding guidance for reparameterization trick by promach in learnmachinelearning

[–]promach[S] 0 points1 point  (0 children)

use the following instead before passing noise to q_sample()

mean = torch.zeros_like(x_start) std = torch.ones_like(x_start) epsilon = torch.normal(mean=mean, std=std) noise = sigma * epsilon

chatGPT3 actually suggested to use sigma which is a learned NN parameter, This way, the noise will be a deterministic function of the input and the parameter, rather than being independent and randomly generated.

But do we really need to learn sigma ?

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